Biomarker compositions and methods

ABSTRACT

Biomarkers can be assessed for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, or the stage or progression of a disease, select candidate treatment regimens for diseases, conditions, disease stages, and stages of a condition, and to determine treatment efficacy. Circulating biomarkers from a bodily fluid can be used in profiling of physiological states or determining phenotypes. These include nucleic acids, protein, and circulating structures such as vesicles, and nucleic acid-protein complexes.

CROSS REFERENCE

This application claims the benefit of U.S. Provisional PatentApplication Nos. 61/497,895, filed Jun. 16, 2011; 61/499,138, filed Jun.20, 2011; 61/501,680, filed Jun. 27, 2011; 61/506,019, filed Jul. 8,2011; 61/506,606, filed Jul. 11, 2011; 61/506,598, filed Jul. 11, 2011;61/507,989, filed Jul. 14, 2011; 61/511,455, filed Jul. 25, 2011;61/523,763, filed Aug. 15, 2011; and 61/526,623, filed Aug. 23, 2011,all of which applications are incorporated herein by reference in theirentirety.

This application is a continuation-in-part of International PatentApplication PCT/US2012/041387, filed Jun. 7, 2012, which applicationclaims the benefit of U.S. Provisional Patent Application Nos.61/494,196, filed Jun. 7, 2011; 61/494,355, filed Jun. 7, 2011; and61/507,989, filed Jul. 14, 2011; all of which applications areincorporated herein by reference in their entirety.

This application is also a continuation-in-part of International PatentApplication PCT/US2012/025741, filed Feb. 17, 2012, which applicationclaims the benefit of U.S. Provisional Patent Application Nos.61/446,313, filed Feb. 24, 2011; 61/501,680, filed Jun. 27, 2011;61/471,417, filed Apr. 4, 2011; 61/523,763, filed Aug. 15, 2011; and61/445,273, filed Feb. 22, 2011; all of which applications areincorporated herein by reference in their entirety.

This application is also a continuation-in-part of International PatentApplication PCT/US2011/048327, filed Aug. 18, 2011, which applicationclaims the benefit of U.S. Provisional Patent Application Nos.61/374,951, filed Aug. 18, 2010; 61/379,670, filed Sep. 2, 2010;61/381,305, filed Sep. 9, 2010; 61/383,305, filed Sep. 15, 2010;61/391,504, filed Oct. 8, 2010; 61/393,823, filed Oct. 15, 2010;61/411,890, filed Nov. 9, 2010; 61/414,870, filed Nov. 17, 2010;61/416,560, filed Nov. 23, 2010; 61/421,851, filed Dec. 10, 2010;61/423,557, filed Dec. 15, 2010; 61/428,196, filed Dec. 29, 2010; all ofwhich applications are incorporated herein by reference in theirentirety.

This application is also a continuation-in-part of International PatentApplication PCT/US2011/026750, filed Mar. 1, 2011, which applicationclaims is a continuation-in-part application of U.S. patent applicationSer. No. 12/591,226, filed Nov. 12, 2009, which claims the benefit ofU.S. Provisional Application Nos. 61/114,045, filed Nov. 12, 2008;61/114,058, filed Nov. 12, 2008; 61/114,065, filed Nov. 13, 2008;61/151,183, filed Feb. 9, 2009; 61/278,049, filed Oct. 2, 2009;61/250,454, filed Oct. 9, 2009; and 61/253,027 filed Oct. 19, 2009; andwhich application also claims the benefit of U.S. ProvisionalApplication Nos. 61/274,124, filed Mar. 1, 2010; 61/357,517, filed Jun.22, 2010; 61/364,785, filed Jul. 15, 2010; all of which applications areincorporated herein by reference in their entirety.

This application is also a continuation-in-part of International PatentApplication PCT/US2011/031479, filed Apr. 6, 2011, which applicationclaims the benefit of U.S. Provisional Patent Application Nos.61/321,392, filed Apr. 6, 2010; 61/321,407, filed Apr. 6, 2010;61/332,174, filed May 6, 2010; 61/348,214, filed May 25, 2010,61/348,685, filed May 26, 2010; 61/354,125, filed Jun. 11, 2010;61/355,387, filed Jun. 16, 2010; 61/356,974, filed Jun. 21, 2010;61/357,517, filed Jun. 22, 2010; 61/362,674, filed Jul. 8, 2010;61/413,377, filed Nov. 12, 2010; 61/322,690, filed Apr. 9, 2010;61/334,547, filed May 13, 2010; 61/364,785, filed Jul. 15, 2010;61/370,088, filed Aug. 2, 2010; 61/379,670, filed Sep. 2, 2010;61/381,305, filed Sep. 9, 2010; 61/383,305, filed Sep. 15, 2010;61/391,504, filed Oct. 8, 2010; 61/393,823, filed Oct. 15, 2010;61/411,890, filed Nov. 9, 2010; and 61/416,560, filed Nov. 23, 2010; allof which applications are incorporated herein by reference in theirentirety.

BACKGROUND

Biomarkers for conditions and diseases such as cancer include biologicalmolecules such as proteins, peptides, lipids, RNAs, DNA and variationsand modifications thereof.

The identification of specific biomarkers, such as DNA, RNA andproteins, can provide biosignatures that are used for the diagnosis,prognosis, or theranosis of conditions or diseases. Biomarkers can bedetected in bodily fluids, including circulating DNA, RNA, proteins, andvesicles. Circulating biomarkers include proteins such as PSA and CA125,and nucleic acids such as SEPT9 DNA and PCA3 messenger RNA (mRNA).Circulating biomarkers can be associated with circulating vesicles.Vesicles are membrane encapsulated structures that are shed from cellsand have been found in a number of bodily fluids, including blood,plasma, serum, breast milk, ascites, bronchoalveolar lavage fluid andurine. Vesicles can take part in the communication between cells astransport vehicles for proteins, RNAs, DNAs, viruses, and prions.MicroRNAs are short RNAs that regulate the transcription and degradationof messenger RNAs. MicroRNAs have been found in bodily fluids and havebeen observed as a component within vesicles shed from tumor cells. Theanalysis of circulating biomarkers associated with diseases, includingvesicles and/or microRNA, can aid in detection of disease or severitythereof, determining predisposition to a disease, as well as makingtreatment decisions.

Vesicles present in a biological sample provide a source of biomarkers,e.g., the markers are present within a vesicle (vesicle payload), or arepresent on the surface of a vesicle. Characteristics of vesicles (e.g.,size, surface antigens, determination of cell-of-origin, payload) canalso provide a diagnostic, prognostic or theranostic readout. Thereremains a need to identify biomarkers that can be used to detect andtreat disease. microRNA, proteins and other biomarkers associated withvesicles as well as the characteristics of a vesicle can provide adiagnosis, prognosis, or theranosis.

The present invention provides methods and systems for characterizing aphenotype by detecting biomarkers that are indicative of disease ordisease progress. The biomarkers can be circulating biomarkers includingwithout limitation vesicle markers, protein, nucleic acids, mRNA, or andmicroRNA. The biomarkers can be nucleic acid-protein complexes.

SUMMARY

Disclosed herein are methods and compositions for characterizing aphenotype by analyzing circulating biomarkers, such as a vesicle,microRNA or protein present in a biological sample. Characterizing aphenotype for a subject or individual may include, but is not limitedto, the diagnosis of a disease or condition, the prognosis of a diseaseor condition, the determination of a disease stage or a condition stage,a drug efficacy, a physiological condition, organ distress or organrejection, disease or condition progression, therapy-related associationto a disease or condition, or a specific physiological or biologicalstate.

In an aspect, the invention provides a method of identifying abiosignature comprising: (a) determining a presence or level of one ormore biomarker in a biological sample, wherein the one or more biomarkercomprises one or more biomarker selected from Table 5; and (b)identifying a biosignature comprising the presence or level of the oneor more biomarker. The methods may further comprise comparing thebiosignature to a reference biosignature, wherein the comparison is usedto characterize a cancer. The reference biosignature can be from asubject without the cancer. The reference biosignature can be from thesubject. For example, the reference biosignature can be from anon-malignant sample from the subject such as normal adjacent tissue, ora different sample taken from the subject over a time course. Thecharacterizing may comprise identifying the presence or risk of thecancer in a subject, or identifying the cancer in a subject asmetastatic or aggressive. The comparing step may comprise determiningwhether the biosignature is altered relative to the referencebiosignature, thereby providing a prognostic, diagnostic or theranosticdetermination for the cancer.

In some embodiments, the one or more biomarker is selected from thegroup consisting of miR-22, let7a, miR-141, miR-182, miR-663, miR-155,mirR-125a-5p, miR-548a-5p, miR-628-5p, miR-517*, miR-450a, miR-920,hsa-miR-619, miR-1913, miR-224*, miR-502-5p, miR-888, miR-376a,miR-542-5p, miR-30b*, miR-1179, and a combination thereof. For example,the one or more biomarker can be selected from the group consisting ofmiR-22, let7a, miR-141, miR-920, miR-450a, and a combination thereof.The biosignature can be used to characterize a prostate cancer.

In other embodiments, the one or more biomarker comprises a messengerRNA (mRNA) selected from the group consisting of the genes in any ofTables 20-24, and a combination thereof. For example, the one or morebiomarker may comprise an mRNA selected from the group consisting ofA2ML1, BAX, C10orf47, C1orf162, CSDA, EIFC3, ETFB, GABARAPL2, GUK1,GZMH, HIST1H3B, HLA-A, HSP90AA1, NRGN, PRDX5, PTMA, RABAC1, RABAGAP1L,RPL22, SAP18, SEPW1, SOX1, and a combination thereof. the one or morebiomarker can also be selected from the group consisting of A2ML1,GABARAPL2, PTMA, RABAC1, SOX1, EFTB, and a combination thereof. Thebiosignature can be used to characterize a prostate cancer.

The one or more biomarker may be selected from the group consisting ofCA-125, CA 19-9, c-reactive protein, CD95, FAP-1, EGFR, EGFRvIII,apolipoprotein AI, apolipoprotein CIII, myoglobin, tenascin C, MSH6,claudin-3, claudin-4, caveolin-1, coagulation factor III, CD9, CD36,CD37, CD53, CD63, CD81, CD136, CD147, Hsp70, Hsp90, Rab13,Desmocollin-1, EMP-2, CK7, CK20, GCDF15, CD82, Rab-5b, Annexin V,MFG-E8, HLA-DR, a miR200 microRNA, miR-200c, and a combination thereof.For example, the one or more biomarker is selected from the groupconsisting of CA-125, CA 19-9, c-reactive protein, CD95, FAP-1, and acombination thereof. The biosignature can be used to characterize anovarian cancer.

In some embodiments, the one or more biomarker is selected from thegroup consisting of hsa-miR-574-3p, hsa-miR-141, hsa-miR-432,hsa-miR-326, hsa-miR-2110, hsa-miR-181a-2*, hsa-miR-107, hsa-miR-301a,hsa-miR-484, hsa-miR-625*, and a combination thereof. The biosignaturecan be used to characterize a prostate cancer, such as to detect thepresence of prostate cancer. The one or more biomarker can also beselected from the group consisting of hsa-miR-582-3p, hsa-miR-20a*,hsa-miR-375, hsa-miR-200b, hsa-miR-379, hsa-miR-572, hsa-miR-513a-5p,hsa-miR-577, hsa-miR-23a*, hsa-miR-1236, hsa-miR-609, hsa-miR-17*,hsa-miR-130b, hsa-miR-619, hsa-miR-624*, hsa-miR-198, and a combinationthereof. The biosignature can be used to characterize a prostate cancer,such as to distinguish metastatic and non-metastatic prostate cancer.

In another embodiment, the one or more biomarker comprises miR-497, anda combination thereof. The biosignature can be used to characterize alung cancer.

The one or more biomarker can be a messenger RNA (mRNA) selected fromthe group consisting of AQP2, BMP5, C16orf86, CXCL13, DST, ERCC1, GNAO1,KLHL5, MAP4K1, NELL2, PENK, PGF, POU3F1, PRSS21, SCML1, SEMG1, SMARCD3,SNAI2, TAF1C, TNNT3, and a combination thereof. The biosignature can beused to characterize a prostate cancer, such as to distinguish aprostate cancer from a non-cancer sample.

In embodiments, the one or more biomarker comprises a messenger RNA(mRNA) selected from the group consisting of ADRB2, ARG2, C22orf32,CYorf14, EIF1AY, FEV, KLK2, KLK4, LRRC26, MAOA, NLGN4Y, PNPLA7, PVRL3,SIM2, SLC30A4, SLC45A3, STX19, TRIM36, TRPM8, and a combination thereof.The biosignature can be used to characterize a prostate cancer, such asto distinguish a prostate cancer from a non-prostate cancer sample suchas a breast cancer sample.

In other embodiments, the one or more biomarker comprises a messengerRNA (mRNA) selected from the group consisting of ADRB2, BAIAP2L2,C19orf33, CDX1, CEACAM6, EEF1A2, ERN2, FAM110B, FOXA2, KLK2, KLK4,LOC389816, LRRC26, MIPOL1, SLC45A3, SPDEF, TRIM31, TRIM36, ZNF613, and acombination thereof. The biosignature can be used to characterize aprostate cancer, such as to distinguish a prostate cancer from anon-prostate cancer sample such as a colorectal cancer sample.

In still other embodiments, the one or more biomarker comprises amessenger RNA (mRNA) selected from the group consisting of ASTN2,CAB39L, CRIP1, FAM110B, FEV, GSTP1, KLK2, KLK4, LOC389816, LRRC26, MUC1,PNPLA7, SIM2, SLC45A3, SPDEF, TRIM36, TRPV6, ZNF613, and a combinationthereof. The biosignature can be used to characterize a prostate cancer,such as to distinguish a prostate cancer from a non-prostate cancersample such as a lung cancer sample.

The one or more biomarker can also be a microRNA that recognizes one ofthe above mRNAs. For example, the microRNA can be selected from thegroup consisting of miRs-26a+b, miR-15, miR-16, miR-195, miR-497,miR-424, miR-206, miR-342-5p, miR-186, miR-1271, miR-600, miR-216b,miR-519 family, miR-203, and a combination thereof.

In another aspect, the invention provides a method comprising: (a)isolating one or more nucleic acid-protein complex from a biologicalsample; (b) determining a presence or level of one or more nucleic acidbiomarker with the one or more nucleic acid-protein complex; and (c)identifying a biosignature comprising the presence or level of the oneor more nucleic acid biomarker. The methods may further comprisecomparing the biosignature to a reference biosignature, wherein thecomparison is used to characterize a cancer. The reference biosignaturecan be from a subject without the cancer. The reference biosignature canbe from the subject. For example, the reference biosignature can be froma non-malignant sample from the subject such as normal adjacent tissue,or a different sample taken from the subject over a time course. Thecharacterizing may comprise identifying the presence or risk of thecancer in a subject, or identifying the cancer in a subject asmetastatic or aggressive. The comparing step may comprise determiningwhether the biosignature is altered relative to the referencebiosignature, thereby providing a prognostic, diagnostic or theranosticdetermination for the cancer.

The nucleic acid-protein complex may comprise one or more proteinselected from the group consisting of one or more Argonaute familymember, Ago1, Ago2, Ago3, Ago4, GW182 (TNRC6A), TNRC6B, TNRC6C,HNRNPA2B1, HNRPAB, ILF2, NCL (Nucleolin), NPM1 (Nucleophosmin), RPL10A,RPL5, RPLP1, RPS12, RPS19, SNRPG, TROVE2, apolipoprotein, apolipoproteinA, apo A-I, apo A-II, apo A-IV, apo A-V, apolipoprotein B, apo B48, apoB100, apolipoprotein C, apo C-I, apo C-II, apo C-III, apo C-IV,apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), apolipoprotein L, APOL1, APOL2, APOL3, APOL4, APOL5, APOL6,APOLD1, and a combination thereof. For example, the one or more proteincan be selected from the group consisting of one or more Argonautefamily member, Ago 1, Ago2, Ago3, Ago4, GW182 (TNRC6A), and acombination thereof. The one or more protein can also be selected fromthe group consisting of Ago2, Apolipoprotein I, GW182 (TNRC6A), and acombination thereof.

The nucleic acid-protein complex may comprise one or more microRNA. Inan embodiment, the one or more microRNA can be one or more microRNA inTable 5. For example, the one or more microRNA can be selected from thegroup consisting of miR-22, miR-16, miR-148a, miR-92a, miR-451, let7a,and a combination thereof. In an embodiment, the nucleic acid-proteincomplex comprises one or more protein selected from the group consistingof Ago2, Apolipoprotein I, GW182 (TNRC6A), and a combination thereof;and the one or more microRNA comprises one or more microRNA selectedfrom the group consisting of miR-16 and miR-92a, and a combinationthereof. The biosignature can be used to characterize a prostate cancer,such as to distinguish a prostate cancer from a non-cancer sample.

In still another aspect, the invention provides a method comprising: (a)detecting one or more protein biomarker in a microvesicle populationfrom a biological sample; (b) determining a presence or level of one ormore one or more nucleic acid biomarker associated with the detectedmicrovesicle population; and (c) identifying a biosignature comprisingthe presence or level of the one or more nucleic acid. For example, thelevel of the one or more one or more nucleic acid biomarker can benormalized to the level of the one or more protein biomarker. Themethods may further comprise comparing the biosignature to a referencebiosignature, wherein the comparison is used to characterize a cancer.The reference biosignature can be from a subject without the cancer. Thereference biosignature can be from the subject. For example, thereference biosignature can be from a non-malignant sample from thesubject such as normal adjacent tissue, or a different sample taken fromthe subject over a time course. The characterizing may compriseidentifying the presence or risk of the cancer in a subject, oridentifying the cancer in a subject as metastatic or aggressive. Thecomparing step may comprise determining whether the biosignature isaltered relative to the reference biosignature, thereby providing aprognostic, diagnostic or theranostic determination for the cancer.

In an embodiment, the one or more protein biomarker comprises one ormore protein selected from the group consisting of PCSA, Ago2, CD9 and acombination thereof. The one or more nucleic acid biomarker can be oneor more microRNA selected from the group consisting of miR-22, miR-16,miR-148a, miR-92a, miR-451, let7a, and a combination thereof. Forexample, the one or more protein biomarker may include PCSA and Ago2;and the one or more nucleic acid biomarker may include miR-22. Asanother example, the one or more protein biomarker may include PCSAand/or CD9; and the one or more nucleic acid biomarker may includemiR-22. In another embodiment, the one or more protein biomarkercomprises PCSA; and the one or more nucleic acid biomarker comprises amessenger RNA (mRNA) selected from any of Tables 22-24. The biosignaturecan be used to characterize a prostate cancer, such as to distinguish aprostate cancer from a non-cancer sample.

The biosignature may comprise a score calculated from a ratio of thelevel of the one or more protein biomarker and one or more nucleic acidbiomarker. In an embodiment, the one or more protein biomarker comprisesPCSA and PSMA and the one or more nucleic acid biomarker comprisesmiR-22 and let7a. In this case, calculating the score may comprisetaking the sum of: (a) a first multiple of the level of miR-22 payloadin the microvesicle subpopulation divided by the level of PCSA proteinassociated with the microvesicle subpopulation; (b) a second multiple ofthe level of let7a payload in the microvesicle subpopulation divided bythe level of PCSA protein associated with the microvesiclesubpopulation; and (c) a third multiple of the level of PSMA proteinassociated with the microvesicle subpopulation. The first, second andthird multiples can be chosen to optimize determining the biosignature.In an embodiment, the first multiple and the second multiple are both10. The third multiple can be 1.

In embodiments of the methods of the system, the biological samplecomprises a bodily fluid. Appropriate bodily fluids without limitationperipheral blood, sera, plasma, ascites, urine, cerebrospinal fluid(CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor,amniotic fluid, cerumen, breast milk, broncheoalveolar lavage fluid,semen, prostatic fluid, cowper's fluid or pre-ejaculatory fluid, femaleejaculate, sweat, fecal matter, hair, tears, cyst fluid, pleural andperitoneal fluid, pericardial fluid, lymph, chyme, chyle, bile,interstitial fluid, menses, pus, sebum, vomit, vaginal secretions,mucosal secretion, stool water, pancreatic juice, lavage fluids fromsinus cavities, bronchopulmonary aspirates, blastocyl cavity fluid, orumbilical cord blood. For example, the biological sample may compriseurine, blood or a blood derivative.

In some embodiments of the methods of the system, the biological samplecomprises a tissue sample, cells from a tissue sample, or circulatingbiomarkers released from such cells. For example, the methods of theinvention can be performed to identify a biosignature for a tissuesample. The biological sample may comprise a cell culture sample, e.g.,the sample may comprise cultured cells and/or culture medium comprisingcirculating biomarkers released from such cultured cells. The tissuesample or culture sample may be a cancer sample may or comprise a tumorsample or tumor cells.

In the methods of the invention, the biological sample may contain oneor more microvesicle. In some embodiments, the one or more biomarker isassociated with the one or more microvesicle. The one or moremicrovesicle may have a diameter between 10 nm and 2000 nm, e.g.,between 20 nm and 1500 nm, between 20 nm and 1000 nm, between 20 nm and500 nm or between 20 nm and 200 nm.

The one or more microvesicle can be isolated from the sample usingmethods disclosed herein or known in the art. In embodiments, the one ormore microvesicle is subjected to size exclusion chromatography, densitygradient centrifugation, differential centrifugation, nanomembraneultrafiltration, immunoabsorbent capture, affinity purification,affinity capture, affinity selection, immunoassay, ELISA, microfluidicseparation, flow cytometry or combinations thereof.

The one or more microvesicle may be contacted with one or more bindingagent. In some embodiments, the one or more binding agent comprises anucleic acid, DNA molecule, RNA molecule, antibody, antibody fragment,aptamer, peptoid, zDNA, peptide nucleic acid (PNA), locked nucleic acid(LNA), lectin, peptide, dendrimer, membrane protein labeling agent,chemical compound, or a combination thereof. For example, the bindingagent can be an antibody or an aptamer. The one or more binding agentcan be used to capture and/or detect the one or more microvesicle. In anembodiment, the one or more binding agent binds to one or more surfaceantigen on the one or more microvesicle. The one or more surface antigencan comprise one or more protein.

The one or more protein can be any useful biomarker on the vesicles ofinterest, such as those disclosed herein. In an embodiment, the one ormore protein comprises one or more cell specific or cancer specificvesicle marker, e.g., CD9, CD63, CD81, PSMA, PCSA, B7H3, EpCam, or aprotein in Tables 4 or 5. The one or more protein may also comprise ageneral vesicle marker, e.g., one or more of a tetraspanin, CD9, CD63,CD81, CD63, CD9, CD81, CD82, CD37, CD53, Rab-5b, Annexin V, MFG-E8, or aprotein in Table 3. In embodiments, the one or more protein comprisesone or more protein in any of Tables 3-5.

The one or more binding agent can be used to capture the one or moremicrovesicle. The captured microvesicles can be used for furtherassessment. For example, the payload within the microvesicles can beassessed. Microvesicle payload comprises one or more nucleic acid,peptide, protein, lipid, antigen, carbohydrate, and/or proteoglycan. Thenucleic acid may comprise one or more DNA, mRNA, microRNA, snoRNA,snRNA, rRNA, tRNA, siRNA, hnRNA, or shRNA. In an embodiment, the one ormore biomarker comprises payload within the one or more capturedmicrovesicle. For example, the one or more biomarker can include mRNApayload. The one or more biomarker can also include microRNA payload.The one or more biomarker can also include protein payload, e.g., innermembrane protein or soluble protein.

The methods of the invention can be performed in vitro, e.g., using anin vitro biological sample or a cell culture sample.

In a further embodiment, the cancer under analysis may be a lung cancerincluding non-small cell lung cancer and small cell lung cancer(including small cell carcinoma (oat cell cancer), mixed smallcell/large cell carcinoma, and combined small cell carcinoma), coloncancer, breast cancer, prostate cancer, liver cancer, pancreas cancer,brain cancer, kidney cancer, ovarian cancer, stomach cancer, skincancer, bone cancer, gastric cancer, breast cancer, pancreatic cancer,glioma, glioblastoma, hepatocellular carcinoma, papillary renalcarcinoma, head and neck squamous cell carcinoma, leukemia, lymphoma,myeloma, or a solid tumor.

In embodiments, the cancer that is characterized by the subject methodscomprises an acute lymphoblastic leukemia; acute myeloid leukemia;adrenocortical carcinoma; AIDS-related cancers; AIDS-related lymphoma;anal cancer; appendix cancer; astrocytomas; atypical teratoid/rhabdoidtumor; basal cell carcinoma; bladder cancer; brain stem glioma; braintumor (including brain stem glioma, central nervous system atypicalteratoid/rhabdoid tumor, central nervous system embryonal tumors,astrocytomas, craniopharyngioma, ependymoblastoma, ependymoma,medulloblastoma, medulloepithelioma, pineal parenchymal tumors ofintermediate differentiation, supratentorial primitive neuroectodermaltumors and pineoblastoma); breast cancer; bronchial tumors; Burkittlymphoma; cancer of unknown primary site; carcinoid tumor; carcinoma ofunknown primary site; central nervous system atypical teratoid/rhabdoidtumor; central nervous system embryonal tumors; cervical cancer;childhood cancers; chordoma; chronic lymphocytic leukemia; chronicmyelogenous leukemia; chronic myeloproliferative disorders; coloncancer; colorectal cancer; craniopharyngioma; cutaneous T-cell lymphoma;endocrine pancreas islet cell tumors; endometrial cancer;ependymoblastoma; ependymoma; esophageal cancer; esthesioneuroblastoma;Ewing sarcoma; extracranial germ cell tumor; extragonadal germ celltumor; extrahepatic bile duct cancer; gallbladder cancer; gastric(stomach) cancer; gastrointestinal carcinoid tumor; gastrointestinalstromal cell tumor; gastrointestinal stromal tumor (GIST); gestationaltrophoblastic tumor; glioma; hairy cell leukemia; head and neck cancer;heart cancer; Hodgkin lymphoma; hypopharyngeal cancer; intraocularmelanoma; islet cell tumors; Kaposi sarcoma; kidney cancer; Langerhanscell histiocytosis; laryngeal cancer; lip cancer; liver cancer;malignant fibrous histiocytoma bone cancer; medulloblastoma;medulloepithelioma; melanoma; Merkel cell carcinoma; Merkel cell skincarcinoma; mesothelioma; metastatic squamous neck cancer with occultprimary; mouth cancer; multiple endocrine neoplasia syndromes; multiplemyeloma; multiple myeloma/plasma cell neoplasm; mycosis fungoides;myelodysplastic syndromes; myeloproliferative neoplasms; nasal cavitycancer; nasopharyngeal cancer; neuroblastoma; Non-Hodgkin lymphoma;nonmelanoma skin cancer; non-small cell lung cancer; oral cancer; oralcavity cancer; oropharyngeal cancer; osteosarcoma; other brain andspinal cord tumors; ovarian cancer; ovarian epithelial cancer; ovariangerm cell tumor; ovarian low malignant potential tumor; pancreaticcancer; papillomatosis; paranasal sinus cancer; parathyroid cancer;pelvic cancer; penile cancer; pharyngeal cancer; pineal parenchymaltumors of intermediate differentiation; pineoblastoma; pituitary tumor;plasma cell neoplasm/multiple myeloma; pleuropulmonary blastoma; primarycentral nervous system (CNS) lymphoma; primary hepatocellular livercancer; prostate cancer; rectal cancer; renal cancer; renal cell(kidney) cancer; renal cell cancer; respiratory tract cancer;retinoblastoma; rhabdomyosarcoma; salivary gland cancer; Sézarysyndrome; small cell lung cancer; small intestine cancer; soft tissuesarcoma; squamous cell carcinoma; squamous neck cancer; stomach(gastric) cancer; supratentorial primitive neuroectodermal tumors;T-cell lymphoma; testicular cancer; throat cancer; thymic carcinoma;thymoma; thyroid cancer; transitional cell cancer; transitional cellcancer of the renal pelvis and ureter; trophoblastic tumor; uretercancer; urethral cancer; uterine cancer; uterine sarcoma; vaginalcancer; vulvar cancer; Waldenström macroglobulinemia; or Wilm's tumor.For example, the cancer can be a prostate cancer, a lung cancer, abreast cancer, a colorectal cancer or an ovarian cancer.

The methods of the invention can be performed in vitro, e.g., using anin vitro biological sample or a cell culture sample.

In an aspect, the invention provides a reagent to carry out any of themethods of the invention. In a related aspect, the invention provides akit comprising a reagent to carry out any of the methods of theinvention. The reagent may be a binding agent, including withoutlimitation an antibody or aptamer to the one or more biomarker. Forexample, the reagent can be a binding agent that is capable of bindingto at least one of the biomarkers in any of Tables 3-5, 9-11, 16-27, 29or 31-32. In some embodiments, the binding agent is labeled directly oris configured to be indirectly labeled.

In another aspect, the invention provides an isolated PCSA+ vesicle. Thevesicle may contain payload comprising one or more microRNA selectedfrom the group consisting of miR-22, let7a, miR-141, miR-182, miR-663,miR-155, mirR-125a-5p, miR-548a-5p, miR-628-5p, miR-517*, miR-450a,miR-920, hsa-miR-619, miR-1913, miR-224*, miR-502-5p, miR-888, miR-376a,miR-542-5p, miR-30b*, miR-1179, and a combination thereof. The vesiclemay also contain payload comprising one or more messenger RNA (mRNA)selected from any of Tables 20-24.

In still another aspect, the invention provides a compositioncomprising: (a) an oligonucleotide comprising a first portion that istethered to a substrate, a second portion that is at least 75%complementary to a microRNA sequence of interest, and a third portioncomprising a label, wherein the second portion is positioned between thefirst and third portions; and (b) a microRNA. The substrate can be asubstrate disclosed herein, e.g., a planar substrate, a column, or abead. In some embodiments, the second portion of the oligonucleotide isat least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% complementary tothe microRNA sequence of interest. The second portion of theoligonucleotide can be at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%,99% or 100% complementary to the microRNA in (b).

In embodiments, the third portion of the oligonucleotide is directlylabeled. In other embodiments, the third portion of the oligonucleotideis indirectly labeled. The third portion of the oligonucleotide can bebiotinylated, e.g., to facilitate binding of a label comprisingstreptavidin such as streptavidin-phycoerytherin (PE) (SAPE). Any usefullabel can be used. For example, the third portion of the oligonucleotidemay comprise a fluorescent label, a radiolabel or an enzymatic label.

In an embodiment, the microRNA in (b) is in a complex with a protein.The protein can be selected from the group consisting of an Argonautefamily member, Ago1, Ago2, Ago3, Ago4, GW182 (TNRC6A), TNRC6B, TNRC6C,HNRNPA2B1, HNRPAB, ILF2, NCL (Nucleolin), NPM1 (Nucleophosmin), RPL10A,RPL5, RPLP1, RPS12, RPS19, SNRPG, TROVE2, apolipoprotein, apolipoproteinA, apo A-I, apo A-II, apo A-IV, apo A-V, apolipoprotein B, apo B48, apoB100, apolipoprotein C, apo C-I, apo C-II, apo C-III, apo C-IV,apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), apolipoprotein L, APOL1, APOL2, APOL3, APOL4, APOL5, APOL6, andAPOLD1. For example, the microRNA can be bound by one or more of Ago1,Ago2, Ago3 and Ago4. The protein can exhibit nucleolytic activity. Theprotein may comprise a recombinant protein. As a non-limiting example,the protein may comprise recombinant Ago2 (rAgo2).

In embodiments, the composition comprises a biological sample. ThemicroRNA may also be isolated from a biological sample. The isolatedmicroRNA may be in a ribonucleoprotein complex with a protein, such asthose above including Ago1, Ago2, Ago3 and Ago4. The biological samplemay comprise a bodily fluid. Non-limiting examples of useful bodilyfluids comprise peripheral blood, sera, plasma, ascites, urine,cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid,aqueous humor, amniotic fluid, cerumen, breast milk, broncheoalveolarlavage fluid, semen, prostatic fluid, cowper's fluid or pre-ejaculatoryfluid, female ejaculate, sweat, fecal matter, hair, tears, cyst fluid,pleural and peritoneal fluid, pericardial fluid, lymph, chyme, chyle,bile, interstitial fluid, menses, pus, sebum, vomit, vaginal secretions,mucosal secretion, stool water, pancreatic juice, lavage fluids fromsinus cavities, bronchopulmonary aspirates, blastocyl cavity fluid, orumbilical cord blood. For example, the bodily fluid can comprise urine,blood or a blood derivative.

In a related aspect, the invention provides a method comprising: (i)providing a composition as taught above; (ii) incubating the compositionunder conditions to allow the microRNA to bind the oligonucleotide; and(iii) detecting an amount of cleavage of the label from the substrate.In an embodiment, detecting an amount of cleavage of the label from thesubstrate comprises detecting an amount of label in contact with thesubstrate before and after step (ii). In another embodiment, cleavage ofthe label from the substrate indicates the presence of a protein incomplex with the microRNA. The protein can be a protein such as thoseabove including Ago1, Ago2, Ago3 and Ago4. The amount of cleavage of thelabel from the substrate can be observed before and after the cleavagereaction has taken place. Alternately, the amount of cleavage of thelabel from the substrate can be observed in real time.

INCORPORATION BY REFERENCE

All publications, patents and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent or patent application wasspecifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A depicts a method of identifying a biosignature comprisingnucleic acid to characterize a phenotype.

FIG. 1B depicts a method of identifying a biosignature of a vesicle orvesicle population to characterize a phenotype.

FIG. 2 illustrates methods of characterizing a phenotype by assessingvesicle biosignatures.

FIG. 2A is a schematic of a planar substrate coated with a captureantibody, which captures vesicles expressing that protein. The captureantibody is for a vesicle protein that is specific or not specific forvesicles derived from diseased cells (“disease vesicle”). The detectionantibody binds to the captured vesicle and provides a fluorescentsignal. The detection antibody can detect an antigen that is generallyassociated with vesicles, or is associated with a cell-of-origin or adisease, e.g., a cancer.

FIG. 2B is a schematic of a bead coated with a capture antibody, whichcaptures vesicles expressing that protein. The capture antibody is for avesicle protein that is specific or not specific for vesicles derivedfrom diseased cells (“disease vesicle”). The detection antibody binds tothe captured vesicle and provides a fluorescent signal. The detectionantibody can detect an antigen that is generally associated withvesicles, or is associated with a cell-of-origin or a disease, e.g., acancer.

FIG. 2C is an example of a screening scheme that can be performed bymultiplexing using the beads as shown in FIG. 2B.

FIG. 2D presents illustrative schemes for capturing and detectingvesicles to characterize a phenotype.

FIG. 2E presents illustrative schemes for assessing vesicle payload tocharacterize a phenotype.

FIG. 3 illustrates a computer system that can be used in some exemplaryembodiments of the invention.

FIG. 4 illustrates a method of depicting results using a bead basedmethod of detecting vesicles from a subject. The number of beadscaptured at a given intensity is an indication of how frequently avesicle expresses the detection protein at that intensity. The moreintense the signal for a given bead, the greater the expression of thedetection protein. The figure shows a normalized graph obtained bycombining normal patients into one curve and cancer patients intoanother, and using bio-statistical analysis to differentiate the curves.Data from each individual is normalized to account for variation in thenumber of beads read by the detection machine, added together, and thennormalized again to account for the different number of samples in eachpopulation.

FIG. 5 illustrates the capture of prostate cancer cells-derived vesiclesfrom plasma with EpCam by assessing TMPRSS2-ERG expression. VCaPpurified vesicles were spiked into normal plasma and then incubated withDynal magnetic beads coated with either the EpCam or isotype controlantibody. RNA was isolated directly from the Dynal beads. Equal volumesof RNA from each sample were used for RT-PCR and subsequent Taqmanassays.

FIG. 6 depicts a bar graph of miR-21 or miR-141 expression with CD9 beadcapture. 1 ml of plasma from prostate cancer patients, 250 ng/ml ofLNCaP, or normal purified vesicles were incubated with CD9 coated Dynalbeads. The RNA was isolated from the beads and the bead supernatant. Onesample (#6) was also uncaptured for comparison. microRNA expression wasmeasured with qRT-PCR and the mean CT values for each sample compared.CD9 capture improves the detection of miR-21 and miR-141 in prostatecancer samples.

FIG. 7 illustrates separation and identification of vesicles using theMoFlo XDP.

FIG. 8 represents a schematic of detecting vesicles in a sample whereinthe presence or level of the desired vesicles are assessed using amicrosphere platform.

FIG. 8A represents a schematic of isolating vesicles from plasma using acolumn based filtering method, wherein the isolated vesicles aresubsequently assessed using a microsphere platform.

FIG. 8B represents a schematic of compression of a membrane of a vesicledue to high-speed centrifugation, such as ultracentrifugation.

FIG. 8C represents a schematic of detecting vesicles bound tomicrospheres using laser detection.

FIG. 9A illustrates the ability of a vesicle bio-signature todiscriminate between normal prostate and PCa samples. Cancer markersincluded EpCam and B7H3. General vesicle markers included CD9, CD81 andCD63. Prostate specific markers included PCSA. PSMA can be used as wellas PCSA. The test was found to be 98% sensitive and 95% specific for PCavs normal samples.

FIG. 9B illustrates mean fluorescence intensity (MFI) on the Y axis forvesicle markers of FIG. 9A in normal and prostate cancer patients.

FIG. 10 is a schematic for a decision tree for a vesicle prostate cancerassay for determining whether a sample is positive for prostate cancer.

FIG. 11 shows the results of a vesicle detection assay for prostatecancer following the decision tree versus detection using elevated PSAlevels.

FIG. 12 illustrates levels of miR-145 in vesicles isolated from controland PCa samples.

FIGS. 13A-13B illustrate the use of microRNA to identify false negativesfrom a vesicle-based diagnostic assay for prostate cancer. FIG. 13Aillustrates a scheme for using miR analysis within vesicles to convertfalse negatives into true positives, thereby improving sensitivity. FIG.13B illustrates a scheme for using miR analysis within vesicles toconvert false positives into true negatives, thereby improvingspecificity. Normalized levels of miR-107 (FIG. 13C) and miR-141 (FIG.13D) are shown on the Y axis for true positives (TP) called by thevesicle diagnostic assay, true negatives (TN) called by the vesiclediagnostic assay, false positives (FP) called by the vesicle diagnosticassay, and false negatives (FN) called by the vesicle diagnostic assay.miR-107 and miR-141 can be used in the schematic shown in FIG. 13A andFIG. 13B.

FIG. 14 illustrates KRAS sequencing in a colorectal cancer (CRC) cellline and patient sample. Samples comprise genomic DNA obtained from thecell line (FIG. 14B) or from a tissue sample from the patient (FIG.14D), or cDNA obtained from RNA payload within vesicles shed from thecell line (FIG. 14A) or from a plasma sample from the patient (FIG.14C).

FIG. 15 illustrates immunoprecipitation of microRNA from human plasma.FIG. 15A shows the mean quantity of miR-16 detected in various fractionsof human plasma. “Beads” are the amount of miR-16 thatco-immunoprecipitated using antibodies to Argonaute2 (Ago2),Apolipoprotein A1 (ApoA1), GW182, and an IgG control. “Dyna” refers toimmunoprecipitation using Dynabead Protein G, whereas “Magna” refers toMagnabind Protein G beads. “Supernt” are the amount of miR-16 detectedin the supernatant of the immunoprecipitation reactions. See Examplesfor details. FIG. 15B is the same as FIG. 15A except that miR-92a wasdetected.

FIG. 16 illustrates flow sorting of complexes stained with PE labeledanti-PCSA antibodies and FITC labeled anti-Ago2 antibodies.

FIG. 17 illustrates detection of microRNA in PCSA/Ago2 positivecomplexes in human plasma samples. The plasma samples were from subjectswith prostate cancer (PrC) or normal controls (normal). FIG. 17A showsmiR-22 copy number in total circulating microvesicle population fromhuman plasma. FIG. 17B shows plasma-derived complexes were sorted usingantibodies against PCSA and Argonaute 2 (Ago2). RNA was isolated and thecopy number of miR-22 was determined in the population of PCSA/Ago2double positive events. FIG. 17C shows the number of PCSA/Ago2 doublepositive events counted by flow cytometry for each plasma sample. FIG.17D shows copy number of miR-22 divided by the total number of PCSA/Ago2positive events for each plasma sample. This yields the copy number ofmiR-22 per PCSA/Ago2 double positive complex.

FIG. 18 illustrates flow cytometry of circulating microvesicles (cMVs)stained with anti-CD9 and/or anti-PCSA. FIG. 18A illustrates analysis ofplasma derived cMVs using labeled antibodies to CD9 and PCSA. FIG. 18Billustrates an enrichment of double positive CD9/PCSA cMVs followingdouble immunoprecipitation with anti-CD9 and anti-PCSA. Compare thedouble positive population in region R7 between FIG. 18A and FIG. 18B.FIG. 18C illustrates analysis of plasma derived cMVs using labeledantibodies to PCSA. FIG. 18D illustrates an enrichment of PCSA positiveevents following a single immunoprecipitation using antibodies againstPCSA. Compare the population in region R4 between FIG. 18C and FIG. 18D.

FIG. 19 illustrates levels of miR-22 in various plasma fractions. FIG.19A illustrates miR-22 copy number in unmodified plasma as determined byABI Taqman detection kit (Assay ID#000398). FIG. 19B illustrates miR-22copy number in the total circulating microvesicle populationconcentrated from patient plasma as determined by ABI Taqman detectionkit. FIG. 19C illustrates miR-22 copy number retained on an anti-PCSAcolumn using starting material that was released from an anti-CD9column. FIG. 19D illustrates copy number of miR-22 relative to thesample-matched PCSA MFI as determined using a bead based assay. Theaverage PCSA MFI signal for cancer and normal input plasma used fordouble immunoprecipitation was 161.67 and 729.17, respectively. FIG. 19Eillustrates copy number of miR-22 in input plasma. FIG. 19F illustratescopy number of miR-22 from cMVs retained on the anti-PCSA column fromthe input plasma in FIG. 19E. FIG. 19G illustrates copy number of miR-22relative to the sample-matched PCSA MFI as determined using a bead basedassay. The average PCSA MFI signal for cancer and normal plasma used forsingle IP was 69.17 and 526.5, respectively.

FIGS. 20A-C illustrate distinguishing PCa and normal (non PCa) samplesusing a score derived from levels of PCSA and PSMA proteins and miR-22and let7a microRNAs associated with cMVs isolated from plasma. FIG. 20Ashows a plot of the score calculated for normal and cancer samples. FIG.20B shows the data of FIG. 20A where the normals are separated intogroups of normal (no prostate conditions), atypia, inflammation and highgrade prostatic intraepithelial neoplasia (high grade PIN, or HGPIN),and the cancers are separated into groups identified for watchfulwaiting (WW) or cancer. FIG. 20C shows an ROC curve generated with thedata. The AUC was 0.77.

FIG. 21 shows illustrative plots for differential expression of miR-920(FIG. 21A) and miR-450a (FIG. 21B) in different sample populations. Thesamples comprised microRNA in PCSA expressing cMVs isolated from plasma.miR-920 is overexpressed in confounding diseases (i.e., high grade PIN(“hgpin”) and inflammatory disease (“inflammation”)) as compared toprostate cancer (“cancer”) and normals (“normal”). miR-450a is downregulated in cancers as compared to the others.

FIG. 22 illustrates dot plots of raw background subtracted fluorescencevalues of selected mRNAs from microarray profiling of vesicle mRNApayload levels. In each plot, the Y axis shows raw background subtractedfluorescence values (Raw BGsub Florescence). The X axis shows dot plotsfor four normal control plasmas and four plasmas from prostate cancerpatients. The mRNAs shown are A2ML1 (FIG. 22A), GABARAPL2 (FIG. 22B),PTMA (FIG. 22C), RABAC1 (FIG. 22D), SOX1 (FIG. 22E), and ETFB (FIG.22F).

FIGS. 23A-23B illustrate levels of miR-141 (FIG. 23A) and miR-375 (FIG.23B) in vesicles isolated from nonrecurring prostate cancer andmetastatic prostate cancer samples, as indicated on the X axis. miRsisolated from vesicles were detected using Taqman assays. P values areshown below the plot. The Y axis shows copy number of miRs detected.

FIGS. 24A and 24B illustrate microRNA miR-497 to distinguish betweenlung cancer and normal (non-lung cancer) using patient blood samples.The Y-axis shows copy number of miR-497 in 0.1 ml of sample. In FIG.24A, the horizontal line indicates a copy number of 1154 copies. In FIG.24B, the horizontal line indicates a copy number of 1356. FIG. 24C is areceiver operating characteristic (ROC) curve for distinguishingnon-small cell lung cancer and normal plasma samples by examining levelsof miR-497 in circulating microvesicles (cMV). The data corresponds toFIG. 24B.

FIG. 25A is an electron micrograph of Vcap-derived microvesicles boundto a glass slide, FIG. 25B is a scanning electron micrograph ofVcap-derived microvesicles, and FIG. 25C is a scanning electronmicrograph of Vcap microvesicles bound to a polystyrene bead coated withpoly-L-lysine. FIG. 25D illustrates blood processing into plasma asspecified in a sample collection protocol.

FIG. 26 illustrates a microRNA functional assay. FIG. 26A shows alabeled synthetic RNA molecule 261-266 and a ribonucleoprotein complexcontaining a target microRNA 267 of interest. FIG. 26B demonstratescleavage of the synthetic RNA molecule at the target recognition site263 when recognized by the ribonucleoprotein complex 267, therebyreleasing the label 265-266. FIGS. 26C-E illustrate inputribonucleoprotein complex from various sources.

DETAILED DESCRIPTION OF THE INVENTION

Disclosed herein are methods and systems for characterizing a phenotypeof a biological sample, e.g., a sample from a cell culture, an organism,or a subject. The phenotype can be characterized by assessing one ormore biomarkers. The biomarkers can be associated with a vesicle orvesicle population, either presented vesicle surface antigens or vesiclepayload. As used herein, vesicle payload comprises entities encapsulatedwithin a vesicle. Vesicle associated biomarkers can comprise bothmembrane bound and soluble biomarkers. The biomarkers can also becirculating biomarkers, such as nucleic acids (e.g., microRNA) orprotein/polypeptide, or functional fragments thereof, assessed in abodily fluid. Unless otherwise specified, the terms “purified” or“isolated” as used herein in reference to vesicles or biomarkercomponents mean partial or complete purification or isolation of suchcomponents from a cell or organism. Furthermore, unless otherwisespecified, reference to vesicle isolation using a binding agent includesbinding a vesicle with the binding agent whether or not such bindingresults in complete isolation of the vesicle apart from other biologicalentities in the starting material.

A method of characterizing a phenotype by analyzing a circulatingbiomarker, e.g., a nucleic acid biomarker, is depicted in scheme 6100Aof FIG. 1A, as a non-limiting illustrative example. In a first step6101, a biological sample is obtained, e.g., a bodily fluid, tissuesample or cell culture. Nucleic acids are isolated from the sample 6103.The nucleic acid can be DNA or RNA, e.g., microRNA. Assessment of suchnucleic acids can provide a biosignature for a phenotype. By samplingthe nucleic acids associated with target phenotype (e.g., disease versushealthy, pre- and post-treatment), one or more nucleic acid markers thatare indicative of the phenotype can be determined. Various aspects ofthe present invention are directed to biosignatures determined byassessing one or more nucleic acid molecules (e.g., microRNA) present inthe sample 6105, where the biosignature corresponds to a predeterminedphenotype 6107. FIG. 1B illustrates a scheme 6100B of using vesicles toisolate the nucleic acid molecules. In one example, a biological sampleis obtained 6102, and one or more vesicles, e.g., vesicles from aparticular cell-of-origin and/or vesicles associated with a particulardisease state, are isolated from the sample 6104. The vesicles areanalyzed 6106 by characterizing surface antigens associated with thevesicles and/or determining the presence or levels of components presentwithin the vesicles (“payload”). Unless specified otherwise, the term“antigen” as used herein refers generally to a biomarker that can bebound by a binding agent, whether the binding agent is an antibody,aptamer, lectin, or other binding agent for the biomarker and regardlessof whether such biomarker illicits an immune response in a host. Vesiclepayload may be protein, including peptides and polypeptides, and/ornucleic acids such as DNA and RNAs. RNA payload includes messenger RNA(mRNA) and microRNA (also referred to herein as miRNA or miR). Aphenotype is characterized based on the biosignature of the vesicles6108. In another illustrative method of the invention, schemes 6100A and6100B are performed together to characterize a phenotype. In such ascheme, vesicles and nucleic acids, e.g., microRNA, are assessed,thereby characterizing the phenotype.

In a related aspect, methods are provided herein for the discovery ofbiomarkers comprising assessing vesicle surface markers or payloadmarkers in one sample and comparing the markers to another sample.Markers that distinguish between the samples can be used as biomarkersaccording to the invention. Such samples can be from a subject or groupof subjects. For example, the groups can be, e.g., known responders andnon-responders to a given treatment for a given disease or disorder.Biomarkers discovered to distinguish the known responders andnon-responders provide a biosignature of whether a subject is likely torespond to a treatment such as a therapeutic agent, e.g., a drug orbiologic.

Phenotypes

Disclosed herein are products and processes for characterizing aphenotype of an individual by analyzing a vesicle such as a membranevesicle. A phenotype can be any observable characteristic or trait of asubject, such as a disease or condition, a disease stage or conditionstage, susceptibility to a disease or condition, prognosis of a diseasestage or condition, a physiological state, or response to therapeutics.A phenotype can result from a subject's gene expression as well as theinfluence of environmental factors and the interactions between the two,as well as from epigenetic modifications to nucleic acid sequences.

A phenotype in a subject can be characterized by obtaining a biologicalsample from a subject and analyzing one or more vesicles from thesample. For example, characterizing a phenotype for a subject orindividual may include detecting a disease or condition (includingpre-symptomatic early stage detecting), determining the prognosis,diagnosis, or theranosis of a disease or condition, or determining thestage or progression of a disease or condition. Characterizing aphenotype can also include identifying appropriate treatments ortreatment efficacy for specific diseases, conditions, disease stages andcondition stages, predictions and likelihood analysis of diseaseprogression, particularly disease recurrence, metastatic spread ordisease relapse. A phenotype can also be a clinically distinct type orsubtype of a condition or disease, such as a cancer or tumor. Phenotypedetermination can also be a determination of a physiological condition,or an assessment of organ distress or organ rejection, such aspost-transplantation. The products and processes described herein allowassessment of a subject on an individual basis, which can providebenefits of more efficient and economical decisions in treatment.

In an aspect, the invention relates to the analysis of a biologicalsample to identify a biosignature to predict whether a subject is likelyto respond to a treatment for a disease or disorder. Characterizating aphenotype includes predicting the responder/non-responder status of thesubject, wherein a responder responds to a treatment for a disease and anon-responder does not respond to the treatment. Vesicles can beanalyzed in the subject and compared to vesicle analysis of previoussubjects that were known to respond or not to a treatment. If thevesicle biosignature in a subject more closely aligns with that ofprevious subjects that were known to respond to the treatment, thesubject can be characterized, or predicted, as a responder to thetreatment. Similarly, if the vesicle biosignature in the subject moreclosely aligns with that of previous subjects that did not respond tothe treatment, the subject can be characterized, or predicted as anon-responder to the treatment. The treatment can be for any appropriatedisease, disorder or other condition. The method can be used in anydisease setting where a vesicle biosignature that correlates withresponder/non-responder status is known.

The term “phenotype” as used herein can mean any trait or characteristicthat is attributed to a vesicle biosignature that is identified usingmethods of the invention. For example, a phenotype can be theidentification of a subject as likely to respond to a treatment, or morebroadly, it can be a diagnostic, prognostic or theranostic determinationbased on a characterized biosignature for a sample obtained from asubject.

In some embodiments, the phenotype comprises a disease or condition suchas those listed in Table 1. For example, the phenotype can comprise thepresence of or likelihood of developing a tumor, neoplasm, or cancer. Acancer detected or assessed by products or processes described hereinincludes, but is not limited to, breast cancer, ovarian cancer, lungcancer, colon cancer, hyperplastic polyp, adenoma, colorectal cancer,high grade dysplasia, low grade dysplasia, prostatic hyperplasia,prostate cancer, melanoma, pancreatic cancer, brain cancer (such as aglioblastoma), hematological malignancy, hepatocellular carcinoma,cervical cancer, endometrial cancer, head and neck cancer, esophagealcancer, gastrointestinal stromal tumor (GIST), renal cell carcinoma(RCC) or gastric cancer. The colorectal cancer can be CRC Dukes B orDukes C-D. The hematological malignancy can be B-Cell ChronicLymphocytic Leukemia, B-Cell Lymphoma-DLBCL, B-CellLymphoma-DLBCL-germinal center-like, B-Cell Lymphoma-DLBCL-activatedB-cell-like, and Burkitt's lymphoma.

The phenotype can be a premalignant condition, such as actinickeratosis, atrophic gastritis, leukoplakia, erythroplasia, LymphomatoidGranulomatosis, preleukemia, fibrosis, cervical dysplasia, uterinecervical dysplasia, xeroderma pigmentosum, Barrett's Esophagus,colorectal polyp, or other abnormal tissue growth or lesion that islikely to develop into a malignant tumor. Transformative viralinfections such as HIV and HPV also present phenotypes that can beassessed according to the invention.

The cancer characterized by the methods of the invention can comprise,without limitation, a carcinoma, a sarcoma, a lymphoma or leukemia, agerm cell tumor, a blastoma, or other cancers. Carcinomas includewithout limitation epithelial neoplasms, squamous cell neoplasmssquamous cell carcinoma, basal cell neoplasms basal cell carcinoma,transitional cell papillomas and carcinomas, adenomas andadenocarcinomas (glands), adenoma, adenocarcinoma, linitis plasticainsulinoma, glucagonoma, gastrinoma, vipoma, cholangiocarcinoma,hepatocellular carcinoma, adenoid cystic carcinoma, carcinoid tumor ofappendix, prolactinoma, oncocytoma, hurthle cell adenoma, renal cellcarcinoma, grawitz tumor, multiple endocrine adenomas, endometrioidadenoma, adnexal and skin appendage neoplasms, mucoepidermoid neoplasms,cystic, mucinous and serous neoplasms, cystadenoma, pseudomyxomaperitonei, ductal, lobular and medullary neoplasms, acinar cellneoplasms, complex epithelial neoplasms, warthin's tumor, thymoma,specialized gonadal neoplasms, sex cord stromal tumor, thecoma,granulosa cell tumor, arrhenoblastoma, sertoli leydig cell tumor, glomustumors, paraganglioma, pheochromocytoma, glomus tumor, nevi andmelanomas, melanocytic nevus, malignant melanoma, melanoma, nodularmelanoma, dysplastic nevus, lentigo maligna melanoma, superficialspreading melanoma, and malignant acral lentiginous melanoma. Sarcomaincludes without limitation Askin's tumor, botryodies, chondrosarcoma,Ewing's sarcoma, malignant hemangio endothelioma, malignant schwannoma,osteosarcoma, soft tissue sarcomas including: alveolar soft partsarcoma, angiosarcoma, cystosarcoma phyllodes, dermatofibrosarcoma,desmoid tumor, desmoplastic small round cell tumor, epithelioid sarcoma,extraskeletal chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma,hemangiopericytoma, hemangiosarcoma, kaposi's sarcoma, leiomyosarcoma,liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibroushistiocytoma, neurofibrosarcoma, rhabdomyosarcoma, and synovialsarcoma.Lymphoma and leukemia include without limitation chronic lymphocyticleukemia/small lymphocytic lymphoma, B-cell prolymphocytic leukemia,lymphoplasmacytic lymphoma (such as waldenstrom macroglobulinemia),splenic marginal zone lymphoma, plasma cell myeloma, plasmacytoma,monoclonal immunoglobulin deposition diseases, heavy chain diseases,extranodal marginal zone B cell lymphoma, also called malt lymphoma,nodal marginal zone B cell lymphoma (nmzl), follicular lymphoma, mantlecell lymphoma, diffuse large B cell lymphoma, mediastinal (thymic) largeB cell lymphoma, intravascular large B cell lymphoma, primary effusionlymphoma, burkitt lymphoma/leukemia, T cell prolymphocytic leukemia, Tcell large granular lymphocytic leukemia, aggressive NK cell leukemia,adult T cell leukemia/lymphoma, extranodal NK/T cell lymphoma, nasaltype, enteropathy-type T cell lymphoma, hepatosplenic T cell lymphoma,blastic NK cell lymphoma, mycosis fungoides/sezary syndrome, primarycutaneous CD30-positive T cell lymphoproliferative disorders, primarycutaneous anaplastic large cell lymphoma, lymphomatoid papulosis,angioimmunoblastic T cell lymphoma, peripheral T cell lymphoma,unspecified, anaplastic large cell lymphoma, classical hodgkin lymphomas(nodular sclerosis, mixed cellularity, lymphocyte-rich, lymphocytedepleted or not depleted), and nodular lymphocyte-predominant hodgkinlymphoma. Germ cell tumors include without limitation germinoma,dysgerminoma, seminoma, nongerminomatous germ cell tumor, embryonalcarcinoma, endodermal sinus turmor, choriocarcinoma, teratoma,polyembryoma, and gonadoblastoma. Blastoma includes without limitationnephroblastoma, medulloblastoma, and retinoblastoma. Other cancersinclude without limitation labial carcinoma, larynx carcinoma,hypopharynx carcinoma, tongue carcinoma, salivary gland carcinoma,gastric carcinoma, adenocarcinoma, thyroid cancer (medullary andpapillary thyroid carcinoma), renal carcinoma, kidney parenchymacarcinoma, cervix carcinoma, uterine corpus carcinoma, endometriumcarcinoma, chorion carcinoma, testis carcinoma, urinary carcinoma,melanoma, brain tumors such as glioblastoma, astrocytoma, meningioma,medulloblastoma and peripheral neuroectodermal tumors, gall bladdercarcinoma, bronchial carcinoma, multiple myeloma, basalioma, teratoma,retinoblastoma, choroidea melanoma, seminoma, rhabdomyosarcoma,craniopharyngeoma, osteosarcoma, chondrosarcoma, myosarcoma,liposarcoma, fibrosarcoma, Ewing sarcoma, and plasmocytoma.

In a further embodiment, the cancer under analysis may be a lung cancerincluding non-small cell lung cancer and small cell lung cancer(including small cell carcinoma (oat cell cancer), mixed smallcell/large cell carcinoma, and combined small cell carcinoma), coloncancer, breast cancer, prostate cancer, liver cancer, pancreas cancer,brain cancer, kidney cancer, ovarian cancer, stomach cancer, skincancer, bone cancer, gastric cancer, breast cancer, pancreatic cancer,glioma, glioblastoma, hepatocellular carcinoma, papillary renalcarcinoma, head and neck squamous cell carcinoma, leukemia, lymphoma,myeloma, or a solid tumor.

In embodiments, the cancer comprises an acute lymphoblastic leukemia;acute myeloid leukemia; adrenocortical carcinoma; AIDS-related cancers;AIDS-related lymphoma; anal cancer; appendix cancer; astrocytomas;atypical teratoid/rhabdoid tumor; basal cell carcinoma; bladder cancer;brain stem glioma; brain tumor (including brain stem glioma, centralnervous system atypical teratoid/rhabdoid tumor, central nervous systemembryonal tumors, astrocytomas, craniopharyngioma, ependymoblastoma,ependymoma, medulloblastoma, medulloepithelioma, pineal parenchymaltumors of intermediate differentiation, supratentorial primitiveneuroectodermal tumors and pineoblastoma); breast cancer; bronchialtumors; Burkitt lymphoma; cancer of unknown primary site; carcinoidtumor; carcinoma of unknown primary site; central nervous systematypical teratoid/rhabdoid tumor; central nervous system embryonaltumors; cervical cancer; childhood cancers; chordoma; chroniclymphocytic leukemia; chronic myelogenous leukemia; chronicmyeloproliferative disorders; colon cancer; colorectal cancer;craniopharyngioma; cutaneous T-cell lymphoma; endocrine pancreas isletcell tumors; endometrial cancer; ependymoblastoma; ependymoma;esophageal cancer; esthesioneuroblastoma; Ewing sarcoma; extracranialgerm cell tumor; extragonadal germ cell tumor; extrahepatic bile ductcancer; gallbladder cancer; gastric (stomach) cancer; gastrointestinalcarcinoid tumor; gastrointestinal stromal cell tumor; gastrointestinalstromal tumor (GIST); gestational trophoblastic tumor; glioma; hairycell leukemia; head and neck cancer; heart cancer; Hodgkin lymphoma;hypopharyngeal cancer; intraocular melanoma; islet cell tumors; Kaposisarcoma; kidney cancer; Langerhans cell histiocytosis; laryngeal cancer;lip cancer; liver cancer; malignant fibrous histiocytoma bone cancer;medulloblastoma; medulloepithelioma; melanoma; Merkel cell carcinoma;Merkel cell skin carcinoma; mesothelioma; metastatic squamous neckcancer with occult primary; mouth cancer; multiple endocrine neoplasiasyndromes; multiple myeloma; multiple myeloma/plasma cell neoplasm;mycosis fungoides; myelodysplastic syndromes; myeloproliferativeneoplasms; nasal cavity cancer; nasopharyngeal cancer; neuroblastoma;Non-Hodgkin lymphoma; nonmelanoma skin cancer; non-small cell lungcancer; oral cancer; oral cavity cancer; oropharyngeal cancer;osteosarcoma; other brain and spinal cord tumors; ovarian cancer;ovarian epithelial cancer; ovarian germ cell tumor; ovarian lowmalignant potential tumor; pancreatic cancer; papillomatosis; paranasalsinus cancer; parathyroid cancer; pelvic cancer; penile cancer;pharyngeal cancer; pineal parenchymal tumors of intermediatedifferentiation; pineoblastoma; pituitary tumor; plasma cellneoplasm/multiple myeloma; pleuropulmonary blastoma; primary centralnervous system (CNS) lymphoma; primary hepatocellular liver cancer;prostate cancer; rectal cancer; renal cancer; renal cell (kidney)cancer; renal cell cancer; respiratory tract cancer; retinoblastoma;rhabdomyosarcoma; salivary gland cancer; Sézary syndrome; small celllung cancer; small intestine cancer; soft tissue sarcoma; squamous cellcarcinoma; squamous neck cancer; stomach (gastric) cancer;supratentorial primitive neuroectodermal tumors; T-cell lymphoma;testicular cancer; throat cancer; thymic carcinoma; thymoma; thyroidcancer; transitional cell cancer; transitional cell cancer of the renalpelvis and ureter; trophoblastic tumor; ureter cancer; urethral cancer;uterine cancer; uterine sarcoma; vaginal cancer; vulvar cancer;Waldenström macroglobulinemia; or Wilm's tumor. The methods of theinvention can be used to characterize these and other cancers. Thus,characterizing a phenotype can be providing a diagnosis, prognosis ortheranosis of one of the cancers disclosed herein.

The phenotype can also be an inflammatory disease, immune disease, orautoimmune disease. For example, the disease may be inflammatory boweldisease (IBD), Crohn's disease (CD), ulcerative colitis (UC), pelvicinflammation, vasculitis, psoriasis, diabetes, autoimmune hepatitis,Multiple Sclerosis, Myasthenia Gravis, Type I diabetes, RheumatoidArthritis, Psoriasis, Systemic Lupus Erythematosis (SLE), Hashimoto'sThyroiditis, Grave's disease, Ankylosing Spondylitis Sjogrens Disease,CREST syndrome, Scleroderma, Rheumatic Disease, organ rejection, PrimarySclerosing Cholangitis, or sepsis.

The phenotype can also comprise a cardiovascular disease, such asatherosclerosis, congestive heart failure, vulnerable plaque, stroke, orischemia. The cardiovascular disease or condition can be high bloodpressure, stenosis, vessel occlusion or a thrombotic event.

The phenotype can also comprise a neurological disease, such as MultipleSclerosis (MS), Parkinson's Disease (PD), Alzheimer's Disease (AD),schizophrenia, bipolar disorder, depression, autism, Prion Disease,Pick's disease, dementia, Huntington disease (HD), Down's syndrome,cerebrovascular disease, Rasmussen's encephalitis, viral meningitis,neurospsychiatric systemic lupus erythematosus (NPSLE), amyotrophiclateral sclerosis, Creutzfeldt-Jacob disease,Gerstmann-Straussler-Scheinker disease, transmissible spongiformencephalopathy, ischemic reperfusion damage (e.g. stroke), brain trauma,microbial infection, or chronic fatigue syndrome. The phenotype may alsobe a condition such as fibromyalgia, chronic neuropathic pain, orperipheral neuropathic pain.

The phenotype may also comprise an infectious disease, such as abacterial, viral or yeast infection. For example, the disease orcondition may be Whipple's Disease, Prion Disease, cirrhosis,methicillin-resistant staphylococcus aureus, HIV, hepatitis, syphilis,meningitis, malaria, tuberculosis, or influenza. Viral proteins, such asHIV or HCV-like particles can be assessed in a vesicle, to characterizea viral condition.

The phenotype can also comprise a perinatal or pregnancy relatedcondition (e.g. preeclampsia or preterm birth), metabolic disease orcondition, such as a metabolic disease or condition associated with ironmetabolism. For example, hepcidin can be assayed in a vesicle tocharacterize an iron deficiency. The metabolic disease or condition canalso be diabetes, inflammation, or a perinatal condition.

The methods of the invention can be used to characterize these and otherdiseases and disorders that can be assessed via a candidate biosignaturecomprising one or a plurality of biomarkers. Thus, characterizing aphenotype can be providing a diagnosis, prognosis or theranosis of oneof the diseases and disorders disclosed herein.

In various embodiments of the invention, a biosignature for any of theconditions or diseases disclosed herein can comprise one or morebiomarkers in one of several different categories of markers, whereinthe categories include one or more of: 1) disease specific biomarkers;2) cell- or tissue-specific biomarkers; 3) vesicle-specific markers(e.g., general vesicle biomarkers); 4. angiogenesis-specific biomarkers;and 5) immunomodulatory biomarkers. Examples of all such markers aredisclosed herein and known to a person having ordinary skill in the art.Furthermore, a biomarker known in the art that is characterized to havea role in a particular disease or condition can be adapted for use as atarget in compositions and methods of the invention. In furtherembodiments, such biomarkers can be all vesicle surface markers, or acombination of vesicle surface markers and vesicle payload markers(i.e., molecules enclosed by a vesicle). In addition, as noted herein,the biological sample assessed can be any biological fluid, or cancomprise individual components present within such biological fluid(e.g., vesicles, nucleic acids, proteins, or complexes thereof).

Subject

One or more phenotypes of a subject can be determined by analyzing oneor more vesicles, such as vesicles, in a biological sample obtained fromthe subject. A subject or patient can include, but is not limited to,mammals such as bovine, avian, canine, equine, feline, ovine, porcine,or primate animals (including humans and non-human primates). A subjectcan also include a mammal of importance due to being endangered, such asa Siberian tiger; or economic importance, such as an animal raised on afarm for consumption by humans, or an animal of social importance tohumans, such as an animal kept as a pet or in a zoo. Examples of suchanimals include, but are not limited to, carnivores such as cats anddogs; swine including pigs, hogs and wild boars; ruminants or ungulatessuch as cattle, oxen, sheep, giraffes, deer, goats, bison, camels orhorses. Also included are birds that are endangered or kept in zoos, aswell as fowl and more particularly domesticated fowl, i.e. poultry, suchas turkeys and chickens, ducks, geese, guinea fowl. Also included aredomesticated swine and horses (including race horses). In addition, anyanimal species connected to commercial activities are also included suchas those animals connected to agriculture and aquaculture and otheractivities in which disease monitoring, diagnosis, and therapy selectionare routine practice in husbandry for economic productivity and/orsafety of the food chain.

The subject can have a pre-existing disease or condition, such ascancer. Alternatively, the subject may not have any known pre-existingcondition. The subject may also be non-responsive to an existing or pasttreatment, such as a treatment for cancer.

Samples

The biological sample obtained from the subject can be any bodily orbiological fluid. For example, the biological sample can be anybiological fluid including but not limited to peripheral blood, sera,plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bonemarrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breastmilk, broncheoalveolar lavage fluid, semen (including prostatic fluid),Cowper's fluid or pre-ejaculatory fluid, female ejaculate, sweat, fecalmatter, hair, tears, cyst fluid, pleural and peritoneal fluid,pericardial fluid, lymph, chyme, chyle, bile, interstitial fluid,menses, pus, sebum, vomit, vaginal secretions, mucosal secretion, stoolwater, pancreatic juice, lavage fluids from sinus cavities,bronchopulmonary aspirates or other lavage fluids. A biological samplemay also include the blastocyl cavity, umbilical cord blood, or maternalcirculation which may be of fetal or maternal origin. The biologicalsample may also be a tissue sample or biopsy from which vesicles andother circulating biomarkers may be obtained. For example, cells fromthe sample can be cultured and vesicles isolated from the culture (seefor example, Example 1). In various embodiments, biomarkers and/orbiosignatures disclosed herein can be assessed directly from suchbiological samples (e.g., identification of presence or levels ofnucleic acid or polypeptide biomarkers or functional fragments thereof)using various methods, such as extraction of nucleic acid molecules fromblood, plasma, serum or any of the foregoing biological samples, use ofprotein or antibody arrays to identify polypeptide (or functionalfragment) biomarker(s), as well as other array, sequencing, PCR andproteomic techniques known in the art for identification and assessmentof nucleic acid and polypeptide molecules. In addition, one or morecomponents present in such samples can be first isolated or enriched andfurther processed to assess the presence or levels of selectedbiomarkers, e.g., to assess a given biosignature. For example,microvesicles can be isolated from a sample prior to profiling themicrovesicles for protein and/or nucleic acid biomarkers.

Table 1 lists illustrative examples of diseases, conditions, orbiological states and a corresponding list of biological samples fromwhich vesicles may be analyzed.

TABLE 1 Examples of Biological Samples for Vesicle Analysis for VariousDiseases, Conditions, or Biological States Illustrative Disease,Condition or Biological State Illustrative Biological SamplesCancers/neoplasms affecting the following tissue Blood, serum, plasma,cerebrospinal fluid (CSF), types/bodily systems: breast, lung, ovarian,colon, urine, sputum, ascites, synovial fluid, semen, nipple rectal,prostate, pancreatic, brain, bone, connective aspirates, saliva,bronchoalveolar lavage fluid, tears, tissue, glands, skin, lymph,nervous system, endocrine, oropharyngeal washes, feces, peritonealfluids, pleural germ cell, genitourinary, hematologic/blood, boneeffusion, sweat, tears, aqueous humor, pericardial marrow, muscle, eye,esophageal, fat tissue, thyroid, fluid, lymph, chyme, chyle, bile, stoolwater, amniotic pituitary, spinal cord, bile duct, heart, gall bladder,fluid, breast milk, pancreatic juice, cerumen, Cowper's bladder, testes,cervical, endometrial, renal, ovarian, fluid or pre-ejaculatory fluid,female ejaculate, digestive/gastrointestinal, stomach, head and neck,interstitial fluid, menses, mucus, pus, sebum, vaginal liver, leukemia,respiratory/thorasic, cancers of lubrication, vomit unknown primary(CUP) Neurodegenerative/neurological disorders: Blood, serum, plasma,CSF, urine Parkinson's disease, Alzheimer's Disease and multiplesclerosis, Schizophrenia, and bipolar disorder, spasticity disorders,epilepsy Cardiovascular Disease: atherosclerosis, Blood, serum, plasma,CSF, urine cardiomyopathy, endocarditis, vunerable plaques, infectionStroke: ischemic, intracerebral hemorrhage, Blood, serum, plasma, CSF,urine subarachnoid hemorrhage, transient ischemic attacks (TIA) Paindisorders: peripheral neuropathic pain and Blood, serum, plasma, CSF,urine chronic neuropathic pain, and fibromyalgia, Autoimmune disease:systemic and localized diseases, Blood, serum, plasma, CSF, urine,synovial fluid rheumatic disease, Lupus, Sjogren's syndrome Digestivesystem abnormalities: Barrett's esophagus, Blood, serum, plasma, CSF,urine irritable bowel syndrome, ulcerative colitis, Crohn's disease,Diverticulosis and Diverticulitis, Celiac Disease Endocrine disorders:diabetes mellitus, various forms Blood, serum, plasma, CSF, urine ofThyroiditis,, adrenal disorders, pituitary disorders Diseases anddisorders of the skin: psoriasis Blood, serum, plasma, CSF, urine,synovial fluid, tears Urological disorders: benign prostatic hypertrophyBlood, serum, plasma, urine (BPH), polycystic kidney disease,interstitial cystitis Hepatic disease/injury: Cirrhosis, induced Blood,serum, plasma, urine hepatotoxicity (due to exposure to natural orsynthetic chemical sources) Kidney disease/injury: acute, sub-acute,chronic Blood, serum, plasma, urine conditions, Podocyte injury, focalsegmental glomerulosclerosis Endometriosis Blood, serum, plasma, urine,vaginal fluids Osteoporosis Blood, serum, plasma, urine, synovial fluidPancreatitis Blood, serum, plasma, urine, pancreatic juice Asthma Blood,serum, plasma, urine, sputum, bronchiolar lavage fluid Allergies Blood,serum, plasma, urine, sputum, bronchiolar lavage fluid Prion-relateddiseases Blood, serum, plasma, CSF, urine Viral Infections: HIV/AIDSBlood, serum, plasma, urine Sepsis Blood, serum, plasma, urine, tears,nasal lavage Organ rejection/transplantation Blood, serum, plasma,urine, various lavage fluids Differentiating conditions: adenoma versusBlood, serum, plasma, urine, sputum, feces, colonic hyperplastic polyp,irritable bowel syndrome (IBS) lavage fluid versus normal, classifyingDukes stages A, B, C, and/or D of colon cancer, adenoma with low-gradehyperplasia versus high-grade hyperplasia, adenoma versus normal,colorectal cancer versus normal, IBS versus. ulcerative colitis (UC)versus Crohn's disease (CD), Pregnancy related physiological states,conditions, or Maternal serum, plasma, amniotic fluid, cord bloodaffiliated diseases: genetic risk, adverse pregnancy outcomes

The methods of the invention can be used to characterize a phenotypeusing a blood sample or blood derivative. Blood derivatives includeplasma and serum. Blood plasma is the liquid component of whole blood,and makes up approximately 55% of the total blood volume. It is composedprimarily of water with small amounts of minerals, salts, ions,nutrients, and proteins in solution. In whole blood, red blood cells,leukocytes, and platelets are suspended within the plasma. Blood serumrefers to blood plasma without fibrinogen or other clotting factors(i.e., whole blood minus both the cells and the clotting factors).

The biological sample may be obtained through a third party, such as aparty not performing the analysis of the biomarkers, whether directassessment of a biological sample or by profiling one or more vesiclesobtained from the biological sample. For example, the sample may beobtained through a clinician, physician, or other health care manager ofa subject from which the sample is derived. Alternatively, thebiological sample may obtained by the same party analyzing the vesicle.In addition, biological samples be assayed, are archived (e.g., frozen)or otherwise stored in under preservative conditions.

The volume of the biological sample used for biomarker analysis can bein the range of between 0.1-20 mL, such as less than about 20, 15, 10,9, 8, 7, 6, 5, 4, 3, 2, 1 or 0.1 mL.

A sample of bodily fluid can be used as a sample for characterizing aphenotype. For example, biomarkers in the sample can be assessed toprovide a diagnosis, prognosis and/or theranosis of a disease. Thebiomarkers can be circulating biomarkers, such as circulating proteinsor nucleic acids. The biomarkers can also be associated with a vesicleor vesicle population. Methods of the invention can be applied to assessone or more vesicles, as well as one or more different vesiclepopulations that may be present in a biological sample or in a subject.Analysis of one or more biomarkers in a biological sample can be used todetermine whether an additional biological sample should be obtained foranalysis. For example, analysis of one or more vesicles in a sample ofbodily fluid can aid in determining whether a tissue biopsy should beobtained.

A sample from a patient can be collected under conditions that preservethe circulating biomarkers and other entities of interest containedtherein for subsequent analysis. In an embodiment, the samples areprocessed using one or more of CellSave Preservative Tubes (Veridex,North Raritan, N.J.), PAXgene Blood DNA Tubes (QIAGEN GmbH, Germany),and RNAlater (QIAGEN GmbH, Germany).

CellSave Preservative Tubes (CellSave tubes) are sterile evacuated bloodcollection tubes. Each tube contains a solution that contains Na2EDTAand a cell preservative. The EDTA absorbs calcium ions, which can reduceor eliminate blood clotting. The preservative preserves the morphologyand cell surface antigen expression of epithelial and other cells. Thecollection and processing can be performed as described in a protocolprovided by the manufacturer. Each tube is evacuated to withdraw venouswhole blood following standard phlebotomy procedures as known to thoseof skill in the art. CellSave tubes are disclosed in U.S. Pat. Nos.5,466,574; 5,512,332; 5,597,531; 5,698,271; 5,985,153; 5,993,665;6,120,856; 6,136,182; 6,365,362; 6,551,843; 6,620,627; 6,623,982;6,645,731; 6,660,159; 6,790,366; 6,861,259; 6,890,426; 7,011,794;7,282,350; 7,332,288; 5,849,517 and 5,459,073, each of which isincorporated by reference in its entirety herein.

The PAXgene Blood DNA Tube (PAXgene tube) is a plastic, evacuated tubefor the collection of whole blood for the isolation of nucleic acids.The tubes can be used for blood collection, transport and storage ofwhole blood specimens and isolation of nucleic acids contained therein,e.g., DNA or RNA. Blood is collected under a standard phlebotomyprotocol into an evacuated tube that contains an additive. Thecollection and processing can be performed as described in a protocolprovided by the manufacturer. PAXgene tubes are disclosed in U.S. Pat.Nos. 5,906,744; 4,741,446; 4,991,104, each of which is incorporated byreference in its entirety herein.

The RNAlater RNA Stabilization Reagent (RNAlater) is used for immediatestabilization of RNA in tissues. RNA can be unstable in harvestedsamples. The aqueous RNAlater reagent permeates tissues and otherbiological samples, thereby stabilizing and protecting the RNA containedtherein. Such protection helps ensure that downstream analyses reflectthe expression profile of the RNA in the tissue or other sample. Thesamples are submerged in an appropriate volume of RNAlater reagentimmediately after harvesting. The collection and processing can beperformed as described in a protocol provided by the manufacturer.According to the manufacturer, the reagent preserves RNA for up to 1 dayat 37° C., 7 days at 18-25° C., or 4 weeks at 2-8° C., allowingprocessing, transportation, storage, and shipping of samples withoutliquid nitrogen or dry ice. The samples can also be placed at −20° C. or−80° C., e.g., for archival storage. The preserved samples can be usedto analyze any type of RNA, including without limitation total RNA,mRNA, and microRNA. RNAlater can also be useful for collecting samplesfor DNA, RNA and protein analysis. RNAlater is disclosed in U.S. Pat.No. 5,346,994, each of which is incorporated by reference in itsentirety herein.

Vesicles

Methods of the invention can include assessing one or more vesicles,including assessing vesicle populations. A vesicle, as used herein, is amembrane vesicle that is shed from cells. Vesicles or membrane vesiclesinclude without limitation: circulating microvesicles (cMVs),microvesicle, exosome, nanovesicle, dexosome, bleb, blebby, prostasome,microparticle, intralumenal vesicle, membrane fragment, intralumenalendosomal vesicle, endosomal-like vesicle, exocytosis vehicle, endosomevesicle, endosomal vesicle, apoptotic body, multivesicular body,secretory vesicle, phospholipid vesicle, liposomal vesicle, argosome,texasome, secresome, tolerosome, melanosome, oncosome, or exocytosedvehicle. Furthermore, although vesicles may be produced by differentcellular processes, the methods of the invention are not limited to orreliant on any one mechanism, insofar as such vesicles are present in abiological sample and are capable of being characterized by the methodsdisclosed herein. Unless otherwise specified, methods that make use of aspecies of vesicle can be applied to other types of vesicles. Vesiclescomprise spherical structures with a lipid bilayer similar to cellmembranes which surrounds an inner compartment which can contain solublecomponents, sometimes referred to as the payload. In some embodiments,the methods of the invention make use of exosomes, which are smallsecreted vesicles of about 40-100 nm in diameter. For a review ofmembrane vesicles, including types and characterizations, see Thery etal., Nat Rev Immunol. 2009 August; 9(8):581-93. Some properties ofdifferent types of vesicles include those in Table 2:

TABLE 2 Vesicle Properties Membrane Exosome- Apoptotic Feature ExosomesMicrovesicles Ectosomes particles like vesicles vesicles Size 50-100 nm100-1,000 nm 50-200 nm 50-80 nm 20-50 nm 50-500 nm Density in 1.13-1.19g/ml 1.04-1.07 g/ml 1.1 g/ml 1.16-1.28 g/ml sucrose EM Cup shapeIrregular Bilamellar Round Irregular Heterogeneous appearance shape,round shape electron structures dense Sedimentation 100,000 g 10,000 g160,000-200,000 g 100,000-200,000 g 175,000 g 1,200 g, 10,000 g, 100,000g Lipid Enriched in Expose PPS Enriched in No lipid compositioncholesterol, cholesterol and rafts sphingomyelin diacylglycerol; andceramide; expose PPS contains lipid rafts; expose PPS Major proteinTetraspanins Integrins, CR1 and CD133; no TNFRI Histones markers (e.g.,CD63, selectins and proteolytic CD63 CD9), Alix, CD40 ligand enzymes; noTSG101 CD63 Intracellular Internal Plasma Plasma Plasma origincompartments membrane membrane membrane (endosomes) Abbreviations:phosphatidylserine (PPS); electron microscopy (EM)

Vesicles include shed membrane bound particles, or “microparticles,”that are derived from either the plasma membrane or an internalmembrane. Vesicles can be released into the extracellular environmentfrom cells. Cells releasing vesicles include without limitation cellsthat originate from, or are derived from, the ectoderm, endoderm, ormesoderm. The cells may have undergone genetic, environmental, and/orany other variations or alterations. For example, the cell can be tumorcells. A vesicle can reflect any changes in the source cell, and therebyreflect changes in the originating cells, e.g., cells having variousgenetic mutations. In one mechanism, a vesicle is generatedintracellularly when a segment of the cell membrane spontaneouslyinvaginates and is ultimately exocytosed (see for example, Keller etal., Immunol. Lett. 107 (2): 102-8 (2006)). Vesicles also includecell-derived structures bounded by a lipid bilayer membrane arising fromboth herniated evagination (blebbing) separation and sealing of portionsof the plasma membrane or from the export of any intracellularmembrane-bounded vesicular structure containing variousmembrane-associated proteins of tumor origin, including surface-boundmolecules derived from the host circulation that bind selectively to thetumor-derived proteins together with molecules contained in the vesiclelumen, including but not limited to tumor-derived microRNAs orintracellular proteins. Blebs and blebbing are further described inCharras et al., Nature Reviews Molecular and Cell Biology, Vol. 9, No.11, p. 730-736 (2008). A vesicle shed into circulation or bodily fluidsfrom tumor cells may be referred to as a “circulating tumor-derivedvesicle.” When such vesicle is an exosome, it may be referred to as acirculating-tumor derived exosome (CTE). In some instances, a vesiclecan be derived from a specific cell of origin. CTE, as with acell-of-origin specific vesicle, typically have one or more uniquebiomarkers that permit isolation of the CTE or cell-of-origin specificvesicle, e.g., from a bodily fluid and sometimes in a specific manner.For example, a cell or tissue specific markers are used to identify thecell of origin. Examples of such cell or tissue specific markers aredisclosed herein and can further be accessed in the Tissue-specific GeneExpression and Regulation (TiGER) Database, available atbioinfo.wilmer.jhu.edu/tiger/; Liu et al. (2008) TiGER: a database fortissue-specific gene expression and regulation. BMC Bioinformatics.9:271; TissueDistributionDBs, available at genomedkfz-heidelberg.de/menu/tissue_db/index.html.

A vesicle can have a diameter of greater than about 10 nm, 20 nm, or 30nm. A vesicle can have a diameter of greater than 40 nm, 50 nm, 100 nm,200 nm, 500 nm, 1000 nm, 1500 nm, 2000 nm or greater than 10,000 nm. Avesicle can have a diameter of about 20-2000 nm, about 20-1500 nm, about30-1000 nm, about 30-800 nm, about 30-200 nm, or about 30-100 nm. Insome embodiments, the vesicle has a diameter of less than 10,000 nm,2000 nm, 1500 nm, 1000 nm, 800 nm, 500 nm, 200 nm, 100 nm, 50 nm, 40 nm,30 nm, 20 nm or less than 10 nm. As used herein the term “about” inreference to a numerical value means that variations of 10% above orbelow the numerical value are within the range ascribed to the specifiedvalue. Typical sizes for various types of vesicles are shown in Table 2.Vesicles can be assessed to measure the diameter of a single vesicle orany number of vesicles. For example, the range of diameters of a vesiclepopulation or an average diameter of a vesicle population can bedetermined. Vesicle diameter can be assessed using methods known in theart, e.g., imaging technologies such as electron microscopy. In anembodiment, a diameter of one or more vesicles is determined usingoptical particle detection. See, e.g., U.S. Pat. No. 7,751,053, entitled“Optical Detection and Analysis of Particles” and issued Jul. 6, 2010;and U.S. Pat. No. 7,399,600, entitled “Optical Detection and Analysis ofParticles” and issued Jul. 15, 2010.

In some embodiments, vesicles are directly assayed from a biologicalsample without prior isolation, purification, or concentration from thebiological sample. For example, the amount of vesicles in the sample canby itself provide a biosignature that provides a diagnostic, prognosticor theranostic determination. Alternatively, the vesicle in the samplemay be isolated, captured, purified, or concentrated from a sample priorto analysis. As noted, isolation, capture or purification as used hereincomprises partial isolation, partial capture or partial purificationapart from other components in the sample. Vesicle isolation can beperformed using various techniques as described herein, e.g.,chromatography, filtration, centrifugation, flow cytometry, affinitycapture (e.g., to a planar surface or bead), and/or using microfluidics.

Vesicles such as exosomes can be assessed to provide a phenotypiccharacterization by comparing vesicle characteristics to a reference. Insome embodiments, surface antigens on a vesicle are assessed. Thesurface antigens can provide an indication of the anatomical originand/or cellular of the vesicles and other phenotypic information, e.g.,tumor status. For example, wherein vesicles found in a patient sample,e.g., a bodily fluid such as blood, serum or plasma, are assessed forsurface antigens indicative of colorectal origin and the presence ofcancer. The surface antigens may comprise any informative biologicalentity that can be detected on the vesicle membrane surface, includingwithout limitation surface proteins, lipids, carbohydrates, and othermembrane components. For example, positive detection of colon derivedvesicles expressing tumor antigens can indicate that the patient hascolorectal cancer. As such, methods of the invention can be used tocharacterize any disease or condition associated with an anatomical orcellular origin, by assessing, for example, disease-specific andcell-specific biomarkers of one or more vesicles obtained from asubject.

In another embodiment, one or more vesicle payloads are assessed toprovide a phenotypic characterization. The payload with a vesiclecomprises any informative biological entity that can be detected asencapsulated within the vesicle, including without limitation proteinsand nucleic acids, e.g., genomic or cDNA, mRNA, or functional fragmentsthereof, as well as microRNAs (miRs). In addition, methods of theinvention are directed to detecting vesicle surface antigens (inaddition or exclusive to vesicle payload) to provide a phenotypiccharacterization. For example, vesicles can be characterized by usingbinding agents (e.g., antibodies or aptamers) that are specific tovesicle surface antigens, and the bound vesicles can be further assessedto identify one or more payload components disclosed therein. Asdescribed herein, the levels of vesicles with surface antigens ofinterest or with payload of interest can be compared to a reference tocharacterize a phenotype. For example, overexpression in a sample ofcancer-related surface antigens or vesicle payload, e.g., a tumorassociated mRNA or microRNA, as compared to a reference, can indicatethe presence of cancer in the sample. The biomarkers assessed can bepresent or absent, increased or reduced based on the selection of thedesired target sample and comparison of the target sample to the desiredreference sample. Non-limiting examples of target samples include:disease; treated/not-treated; different time points, such as a in alongitudinal study; and non-limiting examples of reference sample:non-disease; normal; different time points; and sensitive or resistantto candidate treatment(s).

MicroRNA

Various biomarker molecules can be assessed in biological samples orvesicles obtained from such biological samples. MicroRNAs comprise oneclass biomarkers assessed via methods of the invention. MicroRNAs, alsoreferred to herein as miRNAs or miRs, are short RNA strandsapproximately 21-23 nucleotides in length. MiRNAs are encoded by genesthat are transcribed from DNA but are not translated into protein andthus comprise non-coding RNA. The miRs are processed from primarytranscripts known as pri-miRNA to short stem-loop structures calledpre-miRNA and finally to the resulting single strand miRNA. Thepre-miRNA typically forms a structure that folds back on itself inself-complementary regions. These structures are then processed by thenuclease Dicer in animals or DCL1 in plants. Mature miRNA molecules arepartially complementary to one or more messenger RNA (mRNA) moleculesand can function to regulate translation of proteins. Identifiedsequences of miRNA can be accessed at publicly available databases, suchas www.microRNA.org, www.mirbase.org, orwww.mirz.unibas.ch/cgi/miRNA.cgi.

miRNAs are generally assigned a number according to the namingconvention “mir-[number].” The number of a miRNA is assigned accordingto its order of discovery relative to previously identified miRNAspecies. For example, if the last published miRNA was mir-121, the nextdiscovered miRNA will be named mir-122, etc. When a miRNA is discoveredthat is homologous to a known miRNA from a different organism, the namecan be given an optional organism identifier, of the form [organismidentifier]-mir-[number]. Identifiers include hsa for Homo sapiens andmmu for Mus Musculus. For example, a human homolog to mir-121 might bereferred to as hsa-mir-121 whereas the mouse homolog can be referred toas mmu-mir-121 and the rat homolog can be referred to as mo-mir-121,etc.

Mature microRNA is commonly designated with the prefix “miR” whereas thegene or precursor miRNA is designated with the prefix “mir.” Forexample, mir-121 is a precursor for miR-121. When differing miRNA genesor precursors are processed into identical mature miRNAs, thegenes/precursors can be delineated by a numbered suffix. For example,mir-121-1 and mir-121-2 can refer to distinct genes or precursors thatare processed into miR-121. Lettered suffixes are used to indicateclosely related mature sequences. For example, mir-121a and mir-121b canbe processed to closely related miRNAs miR-121a and miR-121b,respectively. In the context of the invention, any microRNA (miRNA ormiR) designated herein with the prefix mir-* or miR-* is understood toencompass both the precursor and/or mature species, unless otherwiseexplicitly stated otherwise.

Sometimes it is observed that two mature miRNA sequences originate fromthe same precursor. When one of the sequences is more abundant that theother, a “*” suffix can be used to designate the less common variant.For example, miR-121 would be the predominant product whereas miR-121*is the less common variant found on the opposite arm of the precursor.If the predominant variant is not identified, the miRs can bedistinguished by the suffix “5p” for the variant from the 5′ arm of theprecursor and the suffix “3p” for the variant from the 3′ arm. Forexample, miR-121-5p originates from the 5′ arm of the precursor whereasmiR-121-3p originates from the 3′ arm. Less commonly, the 5p and 3pvariants are referred to as the sense (“s”) and anti-sense (“as”) forms,respectively. For example, miR-121-5p may be referred to as miR-121-swhereas miR-121-3p may be referred to as miR-121-as.

The above naming conventions have evolved over time and are generalguidelines rather than absolute rules. For example, the let- andlin-families of miRNAs continue to be referred to by these monikers. Themir/miR convention for precursor/mature forms is also a guideline andcontext should be taken into account to determine which form is referredto. Further details of miR naming can be found at www.mirbase.org orAmbros et al., A uniform system for microRNA annotation, RNA 9:277-279(2003).

Plant miRNAs follow a different naming convention as described in Meyerset al., Plant Cell. 2008 20(12):3186-3190.

A number of miRNAs are involved in gene regulation, and miRNAs are partof a growing class of non-coding RNAs that is now recognized as a majortier of gene control. In some cases, miRNAs can interrupt translation bybinding to regulatory sites embedded in the 3′-UTRs of their targetmRNAs, leading to the repression of translation. Target recognitioninvolves complementary base pairing of the target site with the miRNA'sseed region (positions 2-8 at the miRNA's 5′ end), although the exactextent of seed complementarity is not precisely determined and can bemodified by 3′ pairing. In other cases, miRNAs function like smallinterfering RNAs (siRNA) and bind to perfectly complementary mRNAsequences to destroy the target transcript.

Characterization of a number of miRNAs indicates that they influence avariety of processes, including early development, cell proliferationand cell death, apoptosis and fat metabolism. For example, some miRNAs,such as lin-4, let-7, mir-14, mir-23, and bantam, have been shown toplay critical roles in cell differentiation and tissue development.Others are believed to have similarly important roles because of theirdifferential spatial and temporal expression patterns.

The miRNA database available at miRBase (www.mirbase.org) comprises asearchable database of published miRNA sequences and annotation. Furtherinformation about miRBase can be found in the following articles, eachof which is incorporated by reference in its entirety herein:Griffiths-Jones et al., miRBase: tools for microRNA genomics. NAR 200836(Database Issue):D154-D158; Griffiths-Jones et al., miRBase: microRNAsequences, targets and gene nomenclature. NAR 2006 34(DatabaseIssue):D140-D144; and Griffiths-Jones, S. The microRNA Registry. NAR2004 32(Database Issue):D109-D111. Representative miRNAs contained inRelease 16 of miRBase, made available September 2010.

As described herein, microRNAs are known to be involved in cancer andother diseases and can be assessed in order to characterize a phenotypein a sample. See, e.g., Ferracin et al., Micromarkers: miRNAs in cancerdiagnosis and prognosis, Exp Rev Mol Diag, April 2010, Vol. 10, No. 3,Pages 297-308; Fabbri, miRNAs as molecular biomarkers of cancer, Exp RevMol Diag, May 2010, Vol. 10, No. 4, Pages 435-444. Techniques to isolateand characterize vesicles and miRs are known to those of skill in theart. In addition to the methodology presented herein, additional methodscan be found in U.S. Pat. No. 7,888,035, entitled “METHODS FOR ASSESSINGRNA PATTERNS” and issued Feb. 15, 2011; and International PatentApplication Nos. PCT/US2010/058461, entitled “METHODS AND SYSTEMS FORISOLATING, STORING, AND ANALYZING VESICLES” and filed Nov. 30, 2010; andPCT/US2011/021160, entitled “DETECTION OF GASTROINTESTINAL DISORDERS”and filed Jan. 13, 2011; each of which applications are incorporated byreference herein in their entirety.

Circulating Biomarkers

Circulating biomarkers include biomarkers that are detectable in bodyfluids, such as blood, plasma, serum. Examples of circulating cancerbiomarkers include cardiac troponin T (cTnT), prostate specific antigen(PSA) for prostate cancer and CA125 for ovarian cancer. Circulatingbiomarkers according to the invention include any appropriate biomarkerthat can be detected in bodily fluid, including without limitationprotein, nucleic acids, e.g., DNA, mRNA and microRNA, lipids,carbohydrates and metabolites. Circulating biomarkers can includebiomarkers that are not associated with cells, such as biomarkers thatare membrane associated, embedded in membrane fragments, part of abiological complex, or free in solution. In one embodiment, circulatingbiomarkers are biomarkers that are associated with one or more vesiclespresent in the biological fluid of a subject.

Circulating biomarkers have been identified for use in characterizationof various phenotypes. See, e.g., Ahmed N, et al., Proteomic-basedidentification of haptoglobin-1 precursor as a novel circulatingbiomarker of ovarian cancer. Br. J. Cancer 2004; Mathelin et al.,Circulating proteinic biomarkers and breast cancer, Gynecol Obstet.Fertil. 2006 July-August; 34(7-8):638-46. Epub 2006 Jul. 28; Ye et al.,Recent technical strategies to identify diagnostic biomarkers forovarian cancer. Expert Rev Proteomics. 2007 February; 4(1):121-31;Carney, Circulating oncoproteins HER2/neu, EGFR and CAIX (MN) as novelcancer biomarkers. Expert Rev Mol Diagn. 2007 May; 7(3):309-19; Gagnon,Discovery and application of protein biomarkers for ovarian cancer, CurrOpin Obstet Gynecol. 2008 February; 20(1):9-13; Pasterkamp et al.,Immune regulatory cells: circulating biomarker factories incardiovascular disease. Clin Sci (Lond). 2008 August; 115(4):129-31;Fabbri, miRNAs as molecular biomarkers of cancer, Exp Rev Mol Diag, May2010, Vol. 10, No. 4, Pages 435-444; PCT Patent PublicationWO/2007/088537; U.S. Pat. Nos. 7,745,150 and 7,655,479; U.S. PatentPublications 20110008808, 20100330683, 20100248290, 20100222230,20100203566, 20100173788, 20090291932, 20090239246, 20090226937,20090111121, 20090004687, 20080261258, 20080213907, 20060003465,20050124071, and 20040096915, each of which publication is incorporatedherein by reference in its entirety.

Vesicle Enrichment

A vesicle or a population of vesicles may be isolated, purified,concentrated or otherwise enriched prior to and/or during analysis.Unless otherwise specified, the terms “purified,” “isolated,” or similaras used herein in reference to vesicles or biomarker components areintended to include partial or complete purification or isolation ofsuch components from a cell or organism. Analysis of a vesicle caninclude quantitating the amount one or more vesicle populations of abiological sample. For example, a heterogeneous population of vesiclescan be quantitated, or a homogeneous population of vesicles, such as apopulation of vesicles with a particular biomarker profile, a particularbiosignature, or derived from a particular cell type can be isolatedfrom a heterogeneous population of vesicles and quantitated. Analysis ofa vesicle can also include detecting, quantitatively or qualitatively,one or more particular biomarker profile or biosignature of a vesicle,as described herein.

A vesicle can be stored and archived, such as in a bio-fluid bank andretrieved for analysis as necessary. A vesicle may also be isolated froma biological sample that has been previously harvested and stored from aliving or deceased subject. In addition, a vesicle may be isolated froma biological sample which has been collected as described in King etal., Breast Cancer Res 7(5): 198-204 (2005). A vesicle can be isolatedfrom an archived or stored sample. Alternatively, a vesicle may beisolated from a biological sample and analyzed without storing orarchiving of the sample. Furthermore, a third party may obtain or storethe biological sample, or obtain or store the vesicle for analysis.

An enriched population of vesicles can be obtained from a biologicalsample. For example, vesicles may be concentrated or isolated from abiological sample using size exclusion chromatography, density gradientcentrifugation, differential centrifugation, nanomembraneultrafiltration, immunoabsorbent capture, affinity purification,microfluidic separation, or combinations thereof.

Size exclusion chromatography, such as gel permeation columns,centrifugation or density gradient centrifugation, and filtrationmethods can be used. For example, a vesicle can be isolated bydifferential centrifugation, anion exchange and/or gel permeationchromatography (for example, as described in U.S. Pat. Nos. 6,899,863and 6,812,023), sucrose density gradients, organelle electrophoresis(for example, as described in U.S. Pat. No. 7,198,923), magneticactivated cell sorting (MACS), or with a nanomembrane ultrafiltrationconcentrator. Various combinations of isolation or concentration methodscan be used.

Highly abundant proteins, such as albumin and immunoglobulin, may hinderisolation of vesicles from a biological sample. For example, a vesiclecan be isolated from a biological sample using a system that usesmultiple antibodies that are specific to the most abundant proteinsfound in a biological sample, such as blood. Such a system can remove upto several proteins at once, thus unveiling the lower abundance speciessuch as cell-of-origin specific vesicles.

This type of system can be used for isolation of vesicles frombiological samples such as blood, cerebrospinal fluid or urine. Theisolation of vesicles from a biological sample may also be enhanced byhigh abundant protein removal methods as described in Chromy et al. JProteome Res 2004; 3:1120-1127. In another embodiment, the isolation ofvesicles from a biological sample may also be enhanced by removing serumproteins using glycopeptide capture as described in Zhang et al, MolCell Proteomics 2005; 4:144-155. In addition, vesicles from a biologicalsample such as urine may be isolated by differential centrifugationfollowed by contact with antibodies directed to cytoplasmic oranti-cytoplasmic epitopes as described in Pisitkun et al., Proc NatlAcad Sci USA, 2004; 101:13368-13373.

Isolation or enrichment of a vesicle from a biological sample can alsobe enhanced by use of sonication (for example, by applying ultrasound),detergents, other membrane-activating agents, or any combinationthereof. For example, ultrasonic energy can be applied to a potentialtumor site, and without being bound by theory, release of vesicles froma tissue can be increased, allowing an enriched population of vesiclesthat can be analyzed or assessed from a biological sample using one ormore methods disclosed herein.

Sample Handling

With methods of detecting circulating biomarkers as described here,e.g., antibody affinity isolation, the consistency of the results can beoptimized as necessary using various concentration or isolationprocedures. Such steps can include agitation such as shaking orvortexing, different isolation techniques such as polymer basedisolation, e.g., with PEG, and concentration to different levels duringfiltration or other steps. It will be understood by those in the artthat such treatments can be applied at various stages of testing thevesicle containing sample. In one embodiment, the sample itself, e.g., abodily fluid such as plasma or serum, is vortexed. In some embodiments,the sample is vortexed after one or more sample treatment step, e.g.,vesicle isolation, has occurred. Agitation can occur at some or allappropriate sample treatment steps as desired. Additives can beintroduced at the various steps to improve the process, e.g., to controlaggregation or degradation of the biomarkers of interest.

The results can also be optimized as desirable by treating the samplewith various agents. Such agents include additives to controlaggregation and/or additives to adjust pH or ionic strength. Additivesthat control aggregation include blocking agents such as bovine serumalbumin (BSA) and milk, chaotropic agents such as guanidium hydrochloride, and detergents or surfactants. Useful ionic detergents includesodium dodecyl sulfate (SDS, sodium lauryl sulfate (SLS)), sodiumlaureth sulfate (SLS, sodium lauryl ether sulfate (SLES)), ammoniumlauryl sulfate (ALS), cetrimonium bromide, cetrimonium chloride,cetrimonium stearate, and the like. Useful non-ionic (zwitterionic)detergents include polyoxyethylene glycols, polysorbate 20 (also knownas Tween 20), other polysorbates (e.g., 40, 60, 65, 80, etc), Triton-X(e.g., X100, X114),3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS),CHAPSO, deoxycholic acid, sodium deoxycholate, NP-40, glycosides,octyl-thio-glucosides, maltosides, and the like. In some embodiments,Pluronic F-68, a surfactant shown to reduce platelet aggregation, isused to treat samples containing vesicles during isolation and/ordetection. F68 can be used from a 0.1% to 10% concentration, e.g., a 1%,2.5% or 5% concentration. The pH and/or ionic strength of the solutioncan be adjusted with various acids, bases, buffers or salts, includingwithout limitation sodium chloride (NaCl), phosphate-buffered saline(PBS), tris-buffered saline (TBS), sodium phosphate, potassium chloride,potassium phosphate, sodium citrate and saline-sodium citrate (SSC)buffer. In some embodiments, NaCl is added at a concentration of 0.1% to10%, e.g., 1%, 2.5% or 5% final concentration. In some embodiments,Tween 20 is added to 0.005 to 2% concentration, e.g., 0.05%, 0.25% or0.5% final concentration. Blocking agents for use with the inventioncomprise inert proteins, e.g., milk proteins, non-fat dry milk protein,albumin, BSA, casein, or serum such as newborn calf serum (NBCS), goatserum, rabbit serum or salmon serum. The proteins can be added at a 0.1%to 10% concentration, e.g., 1%, 2%, 3%, 3.5%, 4%, 5%, 6%, 7%, 8%, 9% or10% concentration. In some embodiments, BSA is added to 0.1% to 10%concentration, e.g., 1%, 2%, 3%, 3.5%, 4%, 5%, 6%, 7%, 8%, 9% or 10%concentration. In an embodiment, the sample is treated according to themethodology presented in U.S. patent application Ser. No. 11/632,946,filed Jul. 13, 2005, which application is incorporated herein byreference in its entirety. Commercially available blockers may be used,such as SuperBlock, StartingBlock, Protein-Free from Pierce (a divisionof Thermo Fisher Scientific, Rockford, Ill.). In some embodiments,SSC/detergent (e.g., 20×SSC with 0.5% Tween 20 or 0.1% Triton-X 100) isadded to 0.1% to 10% concentration, e.g., at 1.0% or 5.0% concentration.

The methods of detecting vesicles and other circulating biomarkers canbe optimized as desired with various combinations of protocols andtreatments as described herein. A detection protocol can be optimized byvarious combinations of agitation, isolation methods, and additives. Insome embodiments, the patient sample is vortexed before and afterisolation steps, and the sample is treated with blocking agentsincluding BSA and/or F68. Such treatments may reduce the formation oflarge aggregates or protein or other biological debris and thus providea more consistent detection reading.

Filtration and Ultrafiltration

A vesicle can be isolated from a biological sample by filtering abiological sample from a subject through a filtration module andcollecting from the filtration module a retentate comprising thevesicle, thereby isolating the vesicle from the biological sample. Themethod can comprise filtering a biological sample from a subject througha filtration module comprising a filter; and collecting from thefiltration module a retentate comprising the vesicle, thereby isolatingthe vesicle from the biological sample. In one embodiment, the filterretains molecules greater than about 100 kiloDaltons.

The method can further comprise determining a biosignature of thevesicle. The method can also further comprise applying the retentate toa plurality of substrates, wherein each substrate is coupled to one ormore capture agents, and each subset of the plurality of substratescomprises a different capture agent or combination of capture agentsthan another subset of the plurality of substrates.

Also provided herein is a method of determining a biosignature of avesicle in a sample comprising: filtering a biological sample from asubject with a disorder through a filtration module, collecting from thefiltration module a retentate comprising one or more vesicles, anddetermining a biosignature of the one or more vesicles. In oneembodiment, the filtration module comprises a filter that retainsmolecules greater than about 100 or 150 kiloDaltons.

The method disclosed herein can further comprise characterizing aphenotype in a subject by filtering a biological sample from a subjectthrough a filtration module, collecting from the filtration module aretentate comprising one or more vesicles; detecting a biosignature ofthe one or more vesicles; and characterizing a phenotype in the subjectbased on the biosignature, wherein characterizing is with at least 70%sensitivity. In some embodiments, characterizing comprises determiningan amount of one or more vesicle having the biosignature. Furthermore,the characterizing can be from about 80% to 100% sensitivity.

Also provided herein is a method for multiplex analysis of a pluralityof vesicles. In some embodiments, the method comprises filtering abiological sample from a subject through a filtration module; collectingfrom the filtration module a retentate comprising the plurality ofvesicles, applying the plurality of vesicles to a plurality of captureagents, wherein the plurality of capture agents is coupled to aplurality of substrates, and each subset of the plurality of substratesis differentially labeled from another subset of the plurality ofsubstrates; capturing at least a subset of the plurality of vesicles;and determining a biosignature for at least a subset of the capturedvesicles. In one embodiment, each substrate is coupled to one or morecapture agents, and each subset of the plurality of substrates comprisesa different capture agent or combination of capture agents as comparedto another subset of the plurality of substrates. In some embodiments,at least a subset of the plurality of substrates is intrinsicallylabeled, such as comprising one or more labels. The substrate can be aparticle or bead, or any combination thereof. In some embodiments, thefilter retains molecules greater than 9, 10, 20, 30, 40, 50, 60, 70, 80,90, 100, 150, 200, 250, 300, 350, 400, 450, or 500 kiloDaltons. In oneembodiment, the filtration module comprises a filter that retainsmolecules greater than about 100 or 150 kiloDaltons. In one embodiment,the filtration module comprises a filter that retains molecules greaterthan about 9, 20, 100 or 150 kiloDaltons.

In some embodiments, the method for multiplex analysis of a plurality ofvesicles comprises filtering a biological sample from a subject througha filtration module, wherein the filtration module comprises a filterthat retains molecules greater than about 100 kiloDaltons; collectingfrom the filtration module a retentate comprising the plurality ofvesicles; applying the plurality of vesicles to a plurality of captureagents, wherein the plurality of capture agents is coupled to amicroarray; capturing at least a subset of the plurality of vesicles onthe microarray; and determining a biosignature for at least a subset ofthe captured vesicles. In some embodiments, the filter retains moleculesgreater than 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250,300, 350, 400, 450, or 500 kiloDaltons. In one embodiment, thefiltration module comprises a filter that retains molecules greater thanabout 100 or 150 kiloDaltons. In one embodiment, the filtration modulecomprises a filter that retains molecules greater than about 9, 20, 100or 150 kiloDaltons.

The biological sample can be clarified prior to isolation by filtration.Clarification comprises selective removal of cellular debris and otherundesirable materials. For example, cellular debris and other componentsthat may interfere with detection of the circulating biomarkers can beremoved. The clarification can be by low-speed centrifugation, such asat about 5,000×g, 4,000×g, 3,000×g, 2,000×g, 1,000×g, or less. Thesupernatant, or clarified biological sample, containing the vesicle canthen be collected and filtered to isolate the vesicle from the clarifiedbiological sample. In some embodiments, the biological sample is notclarified prior to isolation of a vesicle by filtration.

In some embodiments, isolation of a vesicle from a sample does not usehigh-speed centrifugation, such as ultracentrifugation. For example,isolation may not require the use of centrifugal speeds, such as about100,000×g or more. In some embodiments, isolation of a vesicle from asample uses speeds of less than 50,000×g, 40,000×g, 30,000×g, 20,000×g,15,000×g, 12,000×g, or 10,000×g.

Any number of applicable filter configurations can be used to filter asample of interest. In some embodiments, the filtration module used toisolate the circulating biomarkers from the biological sample is afiber-based filtration cartridge. For example, the fiber can be a hollowpolymeric fiber, such as a polypropylene hollow fiber. A biologicalsample can be introduced into the filtration module by pumping thesample fluid, such as a biological fluid as disclosed herein, into themodule with a pump device, such as a peristaltic pump. The pump flowrate can vary, such as at about 0.25, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4,4.5, 5, 6, 7, 8, 9, or 10 mL/minute. The flow rate can be adjusted giventhe configuration, e.g., size and throughput, of the filtration module.

The filtration module can be a membrane filtration module. For example,the membrane filtration module can comprise a filter disc membrane, suchas a hydrophilic polyvinylidene difluoride (PVDF) filter disc membranehoused in a stirred cell apparatus (e.g., comprising a magneticstirrer). In some embodiments, the sample moves through the filter as aresult of a pressure gradient established on either side of the filtermembrane.

The filter can comprise a material having low hydrophobic absorptivityand/or high hydrophilic properties. For example, the filter can have anaverage pore size for vesicle retention and permeation of most proteinsas well as a surface that is hydrophilic, thereby limiting proteinadsorption. For example, the filter can comprise a material selectedfrom the group consisting of polypropylene, PVDF, polyethylene,polyfluoroethylene, cellulose, secondary cellulose acetate,polyvinylalcohol, and ethylenevinyl alcohol (EVAL®, Kuraray Co.,Okayama, Japan). Additional materials that can be used in a filterinclude, but are not limited to, polysulfone and polyethersulfone.

The filtration module can have a filter that retains molecules greaterthan about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60,70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250,300, 400, or 500 kiloDaltons (kDa), such as a filter that has a MWCO(molecular weight cut off) of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160,170, 180, 190, 200, 250, 300, 400, or 500 kDa. Ultrafiltration membraneswith a range of MWCO of 9 kDa, 20 kDa and/or 150 kDa can be used. Insome embodiments, the filter within the filtration module has an averagepore diameter of about 0.01 μm to about 0.15 μm, and in some embodimentsfrom about 0.05 μm to about 0.12 μm. In some embodiments, the filter hasan average pore diameter of about 0.06 μm, 0.07 μm, 0.08 μm, 0.09 μm,0.1 μm, 0.11 μm or 0.2 μm.

The filtration module can be a commerically available column, such as acolumn typically used for concentrating proteins or for isolatingproteins (e.g., ultrafiltration). Examples include, but are not limitedto, columns from Millpore (Billerica, Mass.), such as Amicon®centrifugal filters, or from Pierce® (Rockford, Ill.), such as PierceConcentrator filter devices. Useful columns from Pierce includedisposable ultrafiltration centrifugal devices with a MWCO of 9 kDa, 20kDa and/or 150 kDa. These concentrators consist of a high-performanceregenerated cellulose membrane welded to a conical device. The filterscan be as described in U.S. Pat. No. 6,269,957 or 6,357,601, both ofwhich applications are incorporated by reference in their entiretyherein.

The retentate comprising the isolated vesicle can be collected from thefiltration module. The retentate can be collected by flushing theretentate from the filter. Selection of a filter composition havinghydrophilic surface properties, thereby limiting protein adsorption, canbe used, without being bound by theory, for easier collection of theretentate and minimize use of harsh or time-consuming collectiontechniques.

The collected retentate can then be used subsequent analysis, such asassessing a biosignature of one or more vesicles in the retentate, asfurther described herein. The analysis can be directly performed on thecollected retentate. Alternatively, the collected retentate can befurther concentrated or purified, prior to analysis of one or morevesicles. For example, the retentate can be further concentrated orvesicles further isolated from the retentate using size exclusionchromatography, density gradient centrifugation, differentialcentrifugation, immunoabsorbent capture, affinity purification,microfluidic separation, or combinations thereof, such as describedherein. In some embodiments, the retentate can undergo another step offiltration. Alternatively, prior to isolation of a vesicle using afilter, the vesicle is concentrated or isolated using size exclusionchromatography, density gradient centrifugation, differentialcentrifugation, immunoabsorbent capture, affinity purification,microfluidic separation, or combinations thereof.

Combinations of filters can be used for concentrating and isolatingbiomarkers. For example, the biological sample may first be filteredthrough a filter having a porosity or pore size of between about 0.01 μmto about 2 μm, about 0.05 μm to about 1.5 μm, and then the sample isfiltered. For example, prior to filtering a biological sample through afiltration module with a filter that retains molecules greater thanabout 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180,190, 200, 250, 300, 400, or 500 kiloDaltons (kDa), such as a filter thathas a MWCO (molecular weight cut off) of about 50, 60, 70, 80, 90, 100,110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250, 300, 400, or 500,the biological sample may first be filtered through a filter having aporosity or pore size of between about 0.01 μm to about 2 μm, about 0.05μm to about 1.5 μm, In some embodiments, the filter has a pore size ofabout 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7,1.8, 1.9 or 2.0 μm. The filter may be a syringe filter. Thus, in oneembodiment, the method comprises filtering the biological sample througha filter, such as a syringe filter, wherein the syringe filter has aporosity of greater than about 1 μm, prior to filtering the samplethrough a filtration module comprising a filter that retains moleculesgreater than about 100 or 150 kiloDaltons. In an embodiment, the filteris 1.2 μM filter and the filtration is followed by passage of the samplethrough a 7 ml or 20 ml concentrator column with a 150 kDa cutoff.

The filtration module can be a component of a microfluidic device.Microfluidic devices, which may also be referred to as “lab-on-a-chip”systems, biomedical micro-electro-mechanical systems (bioMEMs), ormulticomponent integrated systems, can be used for isolating, andanalyzing, vesicles. Such systems miniaturize and compartmentalizeprocesses that allow for binding of vesicles, detection of biomarkers,and other processes, such as further described herein

A microfluidic device can also be used for isolation of a vesicle bycomprising a filtration module. For example, a microfluidic device canuse one more channels for isolating a vesicle from a biological samplebased on size from a biological sample. A biological sample can beintroduced into one or more microfluidic channels, which selectivelyallows the passage of vesicles. The microfluidic device can furthercomprise binding agents, or more than one filtration module to selectvesicles based on a property of the vesicles, for example, size, shape,deformability, biomarker profile, or biosignature.

Binding Agents

Binding agents (also referred to as binding reagents) include agentsthat are capable of binding a target biomarker. A binding agent can bespecific for the target biomarker, meaning the agent is capable ofbinding a target biomarker. The target can be any useful biomarkerdisclosed herein, such as a biomarker on the vesicle surface. In someembodiments, the target is a single molecule, such as a single protein,so that the binding agent is specific to the single protein. In otherembodiments, the target can be a group of molecules, such as a family orproteins having a similar epitope or moiety, so that the binding agentis specific to the family or group of proteins. The group of moleculescan also be a class of molecules, such as protein, DNA or RNA. Thebinding agent can be a capture agent used to capture a vesicle bybinding a component or biomarker of a vesicle. In some embodiments, acapture agent comprises an antibody or fragment thereof, or an aptamer,that binds to an antigen on a vesicle. The capture agent can beoptionally coupled to a substrate and used to isolate a vesicle, asfurther described herein.

A binding agent is an agent that binds to a circulating biomarker, suchas a vesicle or a component of a vesicle. The binding agent can be usedas a capture agent and/or a detection agent. A capture agent can bindand capture a circulating biomarker, such as by binding a component orbiomarker of a vesicle. For example, the capture agent can be a captureantibody or capture antigen that binds to an antigen on a vesicle. Adetection agent can bind to a circulating biomarker thereby facilitatingdetection of the biomarker. For example, a capture agent comprising anantibody or aptamer that is sequestered to a substrate can be used tocapture a vesicle in a sample, and a detection agent comprising anantibody or aptamer that carries a label can be used to detect thecaptured vesicle via detection of the detection agent's label. In someembodiments, a vesicle is assessed using capture and detection agentsthat recognize the same vesicle biomarkers. For example, a vesiclepopulation can be captured using a tetraspanin such as by using ananti-CD9 antibody bound to a substrate, and the captured vesicles can bedetected using a fluorescently labeled anti-CD9 antibody to label thecaptured vesicles. In other embodiments, a vesicle is assessed usingcapture and detection agents that recognize different vesiclebiomarkers. For example, a vesicle population can be captured using acell-specific marker such as by using an anti-PCSA antibody bound to asubstrate, and the captured vesicles can be detected using afluorescently labeled anti-CD9 antibody to label the captured vesicles.Similarly, the vesicle population can be captured using a generalvesicle marker such as by using an anti-CD9 antibody bound to asubstrate, and the captured vesicles can be detected using afluorescently labeled antibody to a cell-specific or disease specificmarker to label the captured vesicles.

The biomarkers recognized by the binding agent are sometimes referred toherein as an antigen. Unless otherwise specified, antigen as used hereinis meant to encompass any entity that is capable of being bound by abinding agent, regardless of the type of binding agent or theimmunogenicity of the biomarker. The antigen further encompasses afunctional fragment thereof. For example, an antigen can encompass aprotein biomarker capable of being bound by a binding agent, including afragment of the protein that is capable of being bound by a bindingagent.

In one embodiment, a vesicle is captured using a capture agent thatbinds to a biomarker on a vesicle. The capture agent can be coupled to asubstrate and used to isolate a vesicle, as further described herein. Inone embodiment, a capture agent is used for affinity capture orisolation of a vesicle present in a substance or sample.

A binding agent can be used after a vesicle is concentrated or isolatedfrom a biological sample. For example, a vesicle can first be isolatedfrom a biological sample before a vesicle with a specific biosignatureis isolated or detected. The vesicle with a specific biosignature can beisolated or detected using a binding agent for the biomarker. A vesiclewith the specific biomarker can be isolated or detected from aheterogeneous population of vesicles. Alternatively, a binding agent maybe used on a biological sample comprising vesicles without a priorisolation or concentration step. For example, a binding agent is used toisolate or detect a vesicle with a specific biosignature directly from abiological sample.

A binding agent can be a nucleic acid, protein, or other molecule thatcan bind to a component of a vesicle. The binding agent can compriseDNA, RNA, monoclonal antibodies, polyclonal antibodies, Fabs, Fab′,single chain antibodies, synthetic antibodies, aptamers (DNA/RNA),peptoids, zDNA, peptide nucleic acids (PNAs), locked nucleic acids(LNAs), lectins, synthetic or naturally occurring chemical compounds(including but not limited to drugs, labeling reagents), dendrimers, ora combination thereof. For example, the binding agent can be a captureantibody. In embodiments of the invention, the binding agent comprises amembrane protein labeling agent. See, e.g., the membrane proteinlabeling agents disclosed in Alroy et al., U.S. Patent Publication US2005/0158708. In an embodiment, vesicles are isolated or captured asdescribed herein, and one or more membrane protein labeling agent isused to detect the vesicles.

In some instances, a single binding agent can be employed to isolate ordetect a vesicle. In other instances, a combination of different bindingagents may be employed to isolate or detect a vesicle. For example, atleast 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 25, 50, 75 or 100 different binding agents may be used to isolate ordetect a vesicle from a biological sample. Furthermore, the one or moredifferent binding agents for a vesicle can form a biosignature of avesicle, as further described below.

Different binding agents can also be used for multiplexing. For example,isolation or detection of more than one population of vesicles can beperformed by isolating or detecting each vesicle population with adifferent binding agent. Different binding agents can be bound todifferent particles, wherein the different particles are labeled. Inanother embodiment, an array comprising different binding agents can beused for multiplex analysis, wherein the different binding agents aredifferentially labeled or can be ascertained based on the location ofthe binding agent on the array. Multiplexing can be accomplished up tothe resolution capability of the labels or detection method, such asdescribed below. The binding agents can be used to detect the vesicles,such as for detecting cell-of-origin specific vesicles. A binding agentor multiple binding agents can themselves form a binding agent profilethat provides a biosignature for a vesicle. One or more binding agentscan be selected from FIG. 2 of International Patent Application SerialNo. PCT/US2011/031479, entitled “Circulating Biomarkers for Disease” andfiled Apr. 6, 2011, which application is incorporated by reference inits entirety herein. For example, if a vesicle population is detected orisolated using two, three, four or more binding agents in a differentialdetection or isolation of a vesicle from a heterogeneous population ofvesicles, the particular binding agent profile for the vesiclepopulation provides a biosignature for the particular vesiclepopulation. The vesicle can be detected using any number of bindingagents in a multiplex fashion. Thus, the binding agent can also be usedto form a biosignature for a vesicle. The biosignature can be used tocharacterize a phenotype.

The binding agent can be a lectin. Lectins are proteins that bindselectively to polysaccharides and glycoproteins and are widelydistributed in plants and animals. For example, lectins such as thosederived from Galanthus nivalis in the form of Galanthus nivalisagglutinin (“GNA”), Narcissus pseudonarcissus in the form of Narcissuspseudonarcissus agglutinin (“NPA”) and the blue green algae Nostocellipsosporum called “cyanovirin” (Boyd et al. Antimicrob AgentsChemother 41(7): 15211530, 1997; Hammar et al. Ann N Y Acad Sci 724: 166169, 1994; Kaku et al. Arch Biochem Biophys 279(2): 298 304, 1990) canbe used to isolate a vesicle. These lectins can bind to glycoproteinshaving a high mannose content (Chervenak et al. Biochemistry 34(16):5685 5695, 1995). High mannose glycoprotein refers to glycoproteinshaving mannose-mannose linkages in the form of α-1→3 or α-1→6mannose-mannose linkages.

The binding agent can be an agent that binds one or more lectins. Lectincapture can be applied to the isolation of the biomarker cathepsin Dsince it is a glycosylated protein capable of binding the lectinsGalanthus nivalis agglutinin (GNA) and concanavalin A (ConA).

Methods and devices for using lectins to capture vesicles are describedin International Patent Applications PCT/US2010/058461, entitled“METHODS AND SYSTEMS FOR ISOLATING, STORING, AND ANALYZING VESICLES” andfiled Nov. 30, 2010; PCT/US2009/066626, entitled “AFFINITY CAPTURE OFCIRCULATING BIOMARKERS” and filed Dec. 3, 2009; PCT/US2010/037467,entitled “METHODS AND MATERIALS FOR ISOLATING EXOSOMES” and filed Jun.4, 2010; and PCT/US2007/006101, entitled “EXTRACORPOREAL REMOVAL OFMICROVESICULAR PARTICLES” and filed Mar. 9, 2007, each of whichapplications is incorporated by reference herein in its entirety.

The binding agent can be an antibody. For example, a vesicle may beisolated using one or more antibodies specific for one or more antigenspresent on the vesicle. For example, a vesicle can have CD63 on itssurface, and an antibody, or capture antibody, for CD63 can be used toisolate the vesicle. Alternatively, a vesicle derived from a tumor cellcan express EpCam, the vesicle can be isolated using an antibody forEpCam and CD63. Other antibodies for isolating vesicles can include anantibody, or capture antibody, to CD9, PSCA, TNFR, CD63, B7H3, MFG-E8,EpCam, Rab, CD81, STEAP, PCSA, PSMA, or 5T4. Other antibodies forisolating vesicles can include an antibody, or capture antibody, to DR3,STEAP, epha2, TMEM211, MFG-E8, Tissue Factor (TF), unc93A, A33, CD24,NGAL, EpCam, MUC17, TROP2, or TETS.

In some embodiments, the capture agent is an antibody to CD9, CD63,CD81, PSMA, PCSA, B7H3, EpCam, PSCA, ICAM, STEAP, or EGFR. The captureagent can also be used to identify a biomarker of a vesicle. Forexample, a capture agent such as an antibody to CD9 would identify CD9as a biomarker of the vesicle. In some embodiments, a plurality ofcapture agents can be used, such as in multiplex analysis. The pluralityof captures agents can comprise binding agents to one or more of: CD9,CD63, CD81, PSMA, PCSA, B7H3, EpCam, PSCA, ICAM, STEAP, and EGFR. Insome embodiments, the plurality of capture agents comprise bindingagents to CD9, CD63, CD81, PSMA, PCSA, B7H3, MFG-E8, and/or EpCam. Inyet other embodiments, the plurality of capture agents comprises bindingagents to CD9, CD63, CD81, PSMA, PCSA, B7H3, EpCam, PSCA, ICAM, STEAP,and/or EGFR. The plurality of capture agents comprises binding agents toTMEM211, MFG-E8, Tissue Factor (TF), and/or CD24.

The antibodies referenced herein can be immunoglobulin molecules orimmunologically active portions of immunoglobulin molecules, i.e.,molecules that contain an antigen binding site that specifically bindsan antigen and synthetic antibodies. The immunoglobulin molecules can beof any class (e.g., IgG, IgE, IgM, IgD or IgA) or subclass ofimmunoglobulin molecule. Antibodies include, but are not limited to,polyclonal, monoclonal, bispecific, synthetic, humanized and chimericantibodies, single chain antibodies, Fab fragments and F(ab′)₂fragments, Fv or Fv′ portions, fragments produced by a Fab expressionlibrary, anti-idiotypic (anti-Id) antibodies, or epitope-bindingfragments of any of the above. An antibody, or generally any molecule,“binds specifically” to an antigen (or other molecule) if the antibodybinds preferentially to the antigen, and, e.g., has less than about 30%,20%, 10%, 5% or 1% cross-reactivity with another molecule.

The binding agent can also be a polypeptide or peptide. Polypeptide isused in its broadest sense and may include a sequence of subunit aminoacids, amino acid analogs, or peptidomimetics. The subunits may belinked by peptide bonds. The polypeptides may be naturally occurring,processed forms of naturally occurring polypeptides (such as byenzymatic digestion), chemically synthesized or recombinantly expressed.The polypeptides for use in the methods of the present invention may bechemically synthesized using standard techniques. The polypeptides maycomprise D-amino acids (which are resistant to L-amino acid-specificproteases), a combination of D- and L-amino acids, amino acids, orvarious other designer or non-naturally occurring amino acids (e.g.,β-methyl amino acids, Cα-methyl amino acids, and Nα-methyl amino acids,etc.) to convey special properties. Synthetic amino acids may includeornithine for lysine, and norleucine for leucine or isoleucine. Inaddition, the polypeptides can have peptidomimetic bonds, such as esterbonds, to prepare polypeptides with novel properties. For example, apolypeptide may be generated that incorporates a reduced peptide bond,i.e., R₁—CH₂—NH—R₂, where R₁ and R₂ are amino acid residues orsequences. A reduced peptide bond may be introduced as a dipeptidesubunit. Such a polypeptide would be resistant to protease activity, andwould possess an extended half-live in vivo. Polypeptides can alsoinclude peptoids (N-substituted glycines), in which the side chains areappended to nitrogen atoms along the molecule's backbone, rather than tothe α-carbons, as in amino acids. Polypeptides and peptides are intendedto be used interchangeably throughout this application, i.e. where theterm peptide is used, it may also include polypeptides and where theterm polypeptides is used, it may also include peptides. The term“protein” is also intended to be used interchangeably throughout thisapplication with the terms “polypeptides” and “peptides” unlessotherwise specified.

A vesicle may be isolated, captured or detected using a binding agent.The binding agent can be an agent that binds a vesicle “housekeepingprotein,” or general vesicle biomarker. The biomarker can be CD63, CD9,CD81, CD82, CD37, CD53, Rab-5b, Annexin V or MFG-E8. Tetraspanins, afamily of membrane proteins with four transmembrane domains, can be usedas general vesicle markers. The tetraspanins include CD151, CD53, CD37,CD82, CD81, CD9 and CD63. There have been over 30 tetraspaninsidentified in mammals, including the TSPAN1 (TSP-1), TSPAN2 (TSP-2),TSPAN3 (TSP-3), TSPAN4 (TSP-4, NAG-2), TSPAN5 (TSP-5), TSPAN6 (TSP-6),TSPAN7 (CD231, TALLA-1, A15), TSPAN8 (CO-029), TSPAN9 (NET-5), TSPAN10(Oculospanin), TSPAN11 (CD151-like), TSPAN12 (NET-2), TSPAN13 (NET-6),TSPAN14, TSPAN15 (NET-7), TSPAN16 (TM4-B), TSPAN17, TSPAN18, TSPAN19,TSPAN20 (UP1b, UPK1B), TSPAN21 (UP1a, UPK1A), TSPAN22 (RDS, PRPH2),TSPAN23 (ROM1), TSPAN24 (CD151), TSPAN25 (CD53), TSPAN26 (CD37), TSPAN27(CD82), TSPAN28 (CD81), TSPAN29 (CD9), TSPAN30 (CD63), TSPAN31 (SAS),TSPAN32 (TSSC6), TSPAN33, and TSPAN34. Other commonly observed vesiclemarkers include those listed in Table 3. Any of these proteins can beused as vesicle markers. Furthermore, any of the markers disclosedherein or in Table 3 can be selected in identifying a candidatebiosignature for a disease or condition, where the one or more selectedbiomarkers have a direct or indirect role or function in mechanismsinvolved in the disease or condition.

TABLE 3 Proteins Observed in Vesicles from Multiple Cell Types ClassProtein Antigen Presentation MHC class I, MHC class II, Integrins, Alpha4 beta 1, Alpha M beta 2, Beta 2 Immunoglobulin family ICAM1/CD54,P-selection Cell-surface peptidases Dipeptidylpeptidase IV/CD26,Aminopeptidase n/CD13 Tetraspanins CD151, CD53, CD37, CD82, CD81, CD9and CD63 Heat-shock proteins Hsp70, Hsp84/90 Cytoskeletal proteinsActin, Actin-binding proteins, Tubulin Membrane transport and Annexin I,Annexin II, Annexin IV, Annexin V, Annexin VI, fusion RAB7/RAP1B/RADGDISignal transduction Gi2alpha/14-3-3, CBL/LCK Abundant membrane CD63,GAPDH, CD9, CD81, ANXA2, ENO1, SDCBP, MSN, MFGE8, EZR, proteins GK,ANXA1, LAMP2, DPP4, TSG101, HSPA1A, GDI2, CLTC, LAMP1, Cd86, ANPEP,TFRC, SLC3A2, RDX, RAP1B, RAB5C, RAB5B, MYH9, ICAM1, FN1, RAB11B, PIGR,LGALS3, ITGB1, EHD1, CLIC1, ATP1A1, ARF1, RAP1A, P4HB, MUC1, KRT10,HLA-A, FLOT1, CD59, C1orf58, BASP1, TACSTD1, STOM Other TransmembraneCadherins: CDH1, CDH2, CDH12, CDH3, Deomoglein, DSG1, DSG2, DSG3,Proteins DSG4, Desmocollin, DSC1, DSG2, DSG3, Protocadherins, PCDH1,PCDH10, PCDH11x, PCDH11y, PCDH12, FAT, FAT2, FAT4, PCDH15, PCDH17,PCDH18, PCDH19; PCDH20; PCDH7, PCDH8, PCDH9, PCDHA1, PCDHA10, PCDHA11,PCDHA12, PCDHA13, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7,PCDHA8, PCDHA9, PCDHAC1, PCDHAC2, PCDHB1, PCDHB10, PCDHB11, PCDHB12,PCDHB13, PCDHB14, PCDHB15, PCDHB16, PCDHB17, PCDHB18, PCDHB2, PCDHB3,PCDHB4, PCDHB5, PCDHB6, PCDHB7, PCDHB8, PCDHB9, PCDHGA1, PCDHGA10,PCDHGA11, PCDHGA12, PCDHGA2; PCDHGA3, PCDHGA4, PCDHGA5, PCDHGA6,PCDHGA7, PCDHGA8, PCDHGA9, PCDHGB1, PCDHGB2, PCDHGB3, PCDHGB4, PCDHGB5,PCDHGB6, PCDHGB7, PCDHGC3, PCDHGC4, PCDHGC5, CDH9 (cadherin 9, type 2(T1-cadherin)), CDH10 (cadherin 10, type 2 (T2-cadherin)), CDH5 (VE-cadherin (vascular endothelial)), CDH6 (K-cadherin (kidney)), CDH7(cadherin 7, type 2), CDH8 (cadherin 8, type 2), CDH11 (OB-cadherin(osteoblast)), CDH13 (T-cadherin-H-cadherin (heart)), CDH15 (M-cadherin(myotubule)), CDH16 (KSP-cadherin), CDH17 (LI cadherin(liver-intestine)), CDH18 (cadherin 18, type 2), CDH19 (cadherin 19,type 2), CDH20 (cadherin 20, type 2), CDH23 (cadherin 23, (neurosensoryepithelium)), CDH10, CDH11, CDH13, CDH15, CDH16, CDH17, CDH18, CDH19,CDH20, CDH22, CDH23, CDH24, CDH26, CDH28, CDH4, CDH5, CDH6, CDH7, CDH8,CDH9, CELSR1, CELSR2, CELSR3, CLSTN1, CLSTN2, CLSTN3, DCHS1, DCHS2,LOC389118, PCLKC, RESDA1, RET

The binding agent can also be an agent that binds to a vesicle derivedfrom a specific cell type, such as a tumor cell (e.g. binding agent forTissue factor, EpCam, B7H3, RAGE or CD24) or a specific cell-of-origin.The binding agent used to isolate or detect a vesicle can be a bindingagent for an antigen selected from FIG. 1 of International PatentApplication Serial No. PCT/US2011/031479, entitled “CirculatingBiomarkers for Disease” and filed Apr. 6, 2011, which application isincorporated by reference in its entirety herein. The binding agent fora vesicle can also be selected from those listed in FIG. 2 ofInternational Patent Application Serial No. PCT/US2011/031479. Thebinding agent can be for an antigen such as a tetraspanin, MFG-E8,Annexin V, 5T4, B7H3, caveolin, CD63, CD9, E-Cadherin, Tissue factor,MFG-E8, TMEM211, CD24, PSCA, PCSA, PSMA, Rab-5B, STEAP, TNFR1, CD81,EpCam, CD59, CD81, ICAM, EGFR, or CD66. A binding agent for a plateletcan be a glycoprotein such as GpIa-IIa, GpIIb-IIIa, GpIIIb, GpIb, orGpIX. A binding agent can be for an antigen comprisine one or more ofCD9, Erb2, Erb4, CD81, Erb3, MUC16, CD63, DLL4, HLA-Drpe, B7H3, IFNAR,5T4, PCSA, MICB, PSMA, MFG-E8, Muc1, PSA, Muc2, Unc93a, VEGFR2, EpCAM,VEGF A, TMPRSS2, RAGE, PSCA, CD40, Muc17, IL-17-RA, and CD80. Forexample, the binding agent can be one or more of CD9, CD63, CD81, B7H3,PCSA, MFG-E8, MUC2, EpCam, RAGE and Muc17. One or more binding agents,such as one or more binding agents for two or more of the antigens, canbe used for isolating or detecting a vesicle. The binding agent used canbe selected based on the desire of isolating or detecting a vesiclederived from a particular cell type or cell-of-origin specific vesicle.

A binding agent can also be linked directly or indirectly to a solidsurface or substrate. A solid surface or substrate can be any physicallyseparable solid to which a binding agent can be directly or indirectlyattached including, but not limited to, surfaces provided by microarraysand wells, particles such as beads, columns, optical fibers, wipes,glass and modified or functionalized glass, quartz, mica, diazotizedmembranes (paper or nylon), polyformaldehyde, cellulose, celluloseacetate, paper, ceramics, metals, metalloids, semiconductive materials,quantum dots, coated beads or particles, other chromatographicmaterials, magnetic particles; plastics (including acrylics,polystyrene, copolymers of styrene or other materials, polypropylene,polyethylene, polybutylene, polyurethanes, polytetrafluoroethylene(PTFE, Teflon®), etc.), polysaccharides, nylon or nitrocellulose,resins, silica or silica-based materials including silicon and modifiedsilicon, carbon, metals, inorganic glasses, plastics, ceramics,conducting polymers (including polymers such as polypyrole andpolyindole); micro or nanostructured surfaces such as nucleic acidtiling arrays, nanotube, nanowire, or nanoparticulate decoratedsurfaces; or porous surfaces or gels such as methacrylates, acrylamides,sugar polymers, cellulose, silicates, or other fibrous or strandedpolymers. In addition, as is known the art, the substrate may be coatedusing passive or chemically-derivatized coatings with any number ofmaterials, including polymers, such as dextrans, acrylamides, gelatinsor agarose. Such coatings can facilitate the use of the array with abiological sample.

For example, an antibody used to isolate a vesicle can be bound to asolid substrate such as a well, such as commercially available plates(e.g. from Nunc, Milan Italy). Each well can be coated with theantibody. In some embodiments, the antibody used to isolate a vesicle isbound to a solid substrate such as an array. The array can have apredetermined spatial arrangement of molecule interactions, bindingislands, biomolecules, zones, domains or spatial arrangements of bindingislands or binding agents deposited within discrete boundaries. Further,the term array may be used herein to refer to multiple arrays arrangedon a surface, such as would be the case where a surface bore multiplecopies of an array. Such surfaces bearing multiple arrays may also bereferred to as multiple arrays or repeating arrays.

Arrays typically contain addressable moieties that can detect thepresense of an entity, e.g., a vesicle in the sample via a bindingevent. An array may be referred to as a microarray. Arrays ormicroarrays include without limitation DNA microarrays, such as cDNAmicroarrays, oligonucleotide microarrays and SNP microarrays, microRNAarrays, protein microarrays, antibody microarrays, tissue microarrays,cellular microarrays (also called transfection microarrays), chemicalcompound microarrays, and carbohydrate arrays (glycoarrays). DNA arraystypically comprise addressable nucleotide sequences that can bind tosequences present in a sample. MicroRNA arrays, e.g., the MMChips arrayfrom the University of Louisville or commercial systems from Agilent,can be used to detect microRNAs. Protein microarrays can be used toidentify protein-protein interactions, including without limitationidentifying substrates of protein kinases, transcription factorprotein-activation, or to identify the targets of biologically activesmall molecules. Protein arrays may comprise an array of differentprotein molecules, commonly antibodies, or nucleotide sequences thatbind to proteins of interest. In a non-limiting example, a protein arraycan be used to detect vesicles having certain proteins on their surface.Antibody arrays comprise antibodies spotted onto the protein chip thatare used as capture molecules to detect proteins or other biologicalmaterials from a sample, e.g., from cell or tissue lysate solutions. Forexample, antibody arrays can be used to detect vesicle-associatedbiomarkers from bodily fluids, e.g., serum or urine. Tissue microarrayscomprise separate tissue cores assembled in array fashion to allowmultiplex histological analysis. Cellular microarrays, also calledtransfection microarrays, comprise various capture agents, such asantibodies, proteins, or lipids, which can interact with cells tofacilitate their capture on addressable locations. Cellular arrays canalso be used to capture vesicles due to the similarity between a vesicleand cellular membrane. Chemical compound microarrays comprise arrays ofchemical compounds and can be used to detect protein or other biologicalmaterials that bind the compounds. Carbohydrate arrays (glycoarrays)comprise arrays of carbohydrates and can detect, e.g., protein that bindsugar moieties. One of skill will appreciate that similar technologiesor improvements can be used according to the methods of the invention.

A binding agent can also be bound to particles such as beads ormicrospheres. For example, an antibody specific for a component of avesicle can be bound to a particle, and the antibody-bound particle isused to isolate a vesicle from a biological sample. In some embodiments,the microspheres may be magnetic or fluorescently labeled. In addition,a binding agent for isolating vesicles can be a solid substrate itself.For example, latex beads, such as aldehyde/sulfate beads (InterfacialDynamics, Portland, Oreg.) can be used.

A binding agent bound to a magnetic bead can also be used to isolate avesicle. For example, a biological sample such as serum from a patientcan be collected for colon cancer screening. The sample can be incubatedwith anti-CCSA-3 (Colon Cancer-Specific Antigen) coupled to magneticmicrobeads. A low-density microcolumn can be placed in the magneticfield of a MACS Separator and the column is then washed with a buffersolution such as Tris-buffered saline. The magnetic immune complexes canthen be applied to the column and unbound, non-specific material can bediscarded. The CCSA-3 selected vesicle can be recovered by removing thecolumn from the separator and placing it on a collection tube. A buffercan be added to the column and the magnetically labeled vesicle can bereleased by applying the plunger supplied with the column. The isolatedvesicle can be diluted in IgG elution buffer and the complex can then becentrifuged to separate the microbeads from the vesicle. The pelletedisolated cell-of-origin specific vesicle can be resuspended in buffersuch as phosphate-buffered saline and quantitated. Alternatively, due tothe strong adhesion force between the antibody captured cell-of-originspecific vesicle and the magnetic microbeads, a proteolytic enzyme suchas trypsin can be used for the release of captured vesicles without theneed for centrifugation. The proteolytic enzyme can be incubated withthe antibody captured cell-of-origin specific vesicles for at least atime sufficient to release the vesicles.

A binding agent, such as an antibody, for isolating vesicles ispreferably contacted with the biological sample comprising the vesiclesof interest for at least a time sufficient for the binding agent to bindto a component of the vesicle. For example, an antibody may be contactedwith a biological sample for various intervals ranging from secondsdays, including but not limited to, about 10 minutes, 30 minutes, 1hour, 3 hours, 5 hours, 7 hours, 10 hours, 15 hours, 1 day, 3 days, 7days or 10 days.

A binding agent, such as an antibody specific to an antigen listed inFIG. 1 of International Patent Application Serial No. PCT/US2011/031479,entitled “Circulating Biomarkers for Disease” and filed Apr. 6, 2011,which application is incorporated by reference in its entirety herein,or a binding agent listed in FIG. 2 of International Patent ApplicationSerial No. PCT/US2011/031479, can be labeled to facilitate detection.Appropriate labels include without limitation a magnetic label, afluorescent moiety, an enzyme, a chemiluminescent probe, a metalparticle, a non-metal colloidal particle, a polymeric dye particle, apigment molecule, a pigment particle, an electrochemically activespecies, semiconductor nanocrystal or other nanoparticles includingquantum dots or gold particles, fluorophores, quantum dots, orradioactive labels. Protein labels include green fluorescent protein(GFP) and variants thereof (e.g., cyan fluorescent protein and yellowfluorescent protein); and luminescent proteins such as luciferase, asdescribed below. Radioactive labels include without limitationradioisotopes (radionuclides), such as ³H, ¹¹C, ¹⁴C, ¹⁸F, ³²P, ³⁵S,⁶⁴Cu, ⁶⁸Ga, ⁸⁶Y, ⁹⁹Tc, ¹¹¹In, ¹²³I, ¹²⁴I, ¹²⁵I, ¹³¹I, ¹³³Xe, ¹⁷⁷Lu,²¹¹At, or ²¹³Bi. Fluorescent labels include without limitation a rareearth chelate (e.g., europium chelate), rhodamine; fluorescein typesincluding without limitation FITC, 5-carboxyfluorescein, 6-carboxyfluorescein; a rhodamine type including without limitation TAMRA;dansyl; Lissamine; cyanines; phycoerythrins; Texas Red; Cy3, Cy5,dapoxyl, NBD, Cascade Yellow, dansyl, PyMPO, pyrene,7-diethylaminocoumarin-3-carboxylic acid and other coumarin derivatives,Marina Blue™, Pacific Blue™, Cascade Blue™, 2-anthracenesulfonyl, PyMPO,3,4,9,10-perylene-tetracarboxylic acid, 2,7-difluorofluorescein (OregonGreen™ 488-X), 5-carboxyfluorescein, Texas Red™-X, Alexa Fluor 430,5-carboxytetramethylrhodamine (5-TAMRA), 6-carboxytetramethylrhodamine(6-TAMRA), BODIPY FL, bimane, and Alexa Fluor 350, 405, 488, 500, 514,532, 546, 555, 568, 594, 610, 633, 647, 660, 680, 700, and 750, andderivatives thereof, among many others. See, e.g., “The Handbook—A Guideto Fluorescent Probes and Labeling Technologies,” Tenth Edition,available on the internet at probes (dot) invitrogen (dot) com/handbook.The fluorescent label can be one or more of FAM, dRHO, 5-FAM, 6FAM,dR6G, JOE, HEX, VIC, TET, dTAMRA, TAMRA, NED, dROX, PET, BHQ, Gold540and LIZ.

A binding agent can be directly or indirectly labeled, e.g., the labelis attached to the antibody through biotin-streptavidin. Alternatively,an antibody is not labeled, but is later contacted with a secondantibody that is labeled after the first antibody is bound to an antigenof interest.

For example, various enzyme-substrate labels are available or disclosed(see for example, U.S. Pat. No. 4,275,149). The enzyme generallycatalyzes a chemical alteration of a chromogenic substrate that can bemeasured using various techniques. For example, the enzyme may catalyzea color change in a substrate, which can be measuredspectrophotometrically. Alternatively, the enzyme may alter thefluorescence or chemiluminescence of the substrate. Examples ofenzymatic labels include luciferases (e.g., firefly luciferase andbacterial luciferase; U.S. Pat. No. 4,737,456), luciferin,2,3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidasesuch as horseradish peroxidase (HRP), alkaline phosphatase (AP),β-galactosidase, glucoamylase, lysozyme, saccharide oxidases (e.g.,glucose oxidase, galactose oxidase, and glucose-6-phosphatedehydrogenase), heterocyclic oxidases (such as uricase and xanthineoxidase), lactoperoxidase, microperoxidase, and the like. Examples ofenzyme-substrate combinations include, but are not limited to,horseradish peroxidase (HRP) with hydrogen peroxidase as a substrate,wherein the hydrogen peroxidase oxidizes a dye precursor (e.g.,orthophenylene diamine (OPD) or 3,3′,5,5′-tetramethylbenzidinehydrochloride (TMB)); alkaline phosphatase (AP) with para-nitrophenylphosphate as chromogenic substrate; and β-D-galactosidase (β-D-Gal) witha chromogenic substrate (e.g., p-nitrophenyl-β-D-galactosidase) orfluorogenic substrate 4-methylumbelliferyl-β-D-galactosidase.

Depending on the method of isolation or detection used, the bindingagent may be linked to a solid surface or substrate, such as arrays,particles, wells and other substrates described above. Methods fordirect chemical coupling of antibodies, to the cell surface are known inthe art, and may include, for example, coupling using glutaraldehyde ormaleimide activated antibodies. Methods for chemical coupling usingmultiple step procedures include biotinylation, coupling oftrinitrophenol (TNP) or digoxigenin using for example succinimide estersof these compounds. Biotinylation can be accomplished by, for example,the use of D-biotinyl-N-hydroxysuccinimide. Succinimide groups reacteffectively with amino groups at pH values above 7, and preferentiallybetween about pH 8.0 and about pH 8.5. Biotinylation can be accomplishedby, for example, treating the cells with dithiothreitol followed by theaddition of biotin maleimide.

Flow Cytometry

Isolation or detection of a vesicle using a particle such as a bead ormicrosphere can also be performed using flow cytometry. Flow cytometrycan be used for sorting microscopic particles suspended in a stream offluid. As particles pass through they can be selectively charged and ontheir exit can be deflected into separate paths of flow. It is thereforepossible to separate populations from an original mix, such as abiological sample, with a high degree of accuracy and speed. Flowcytometry allows simultaneous multiparametric analysis of the physicaland/or chemical characteristics of single cells flowing through anoptical/electronic detection apparatus. A beam of light, usually laserlight, of a single frequency (color) is directed onto a hydrodynamicallyfocused stream of fluid. A number of detectors are aimed at the pointwhere the stream passes through the light beam; one in line with thelight beam (Forward Scatter or FSC) and several perpendicular to it(Side Scatter or SSC) and one or more fluorescent detectors.

Each suspended particle passing through the beam scatters the light insome way, and fluorescent chemicals in the particle may be excited intoemitting light at a lower frequency than the light source. Thiscombination of scattered and fluorescent light is picked up by thedetectors, and by analyzing fluctuations in brightness at each detector(one for each fluorescent emission peak), it is possible to deducevarious facts about the physical and chemical structure of eachindividual particle. FSC correlates with the cell size and SSC dependson the inner complexity of the particle, such as shape of the nucleus,the amount and type of cytoplasmic granules or the membrane roughness.Some flow cytometers have eliminated the need for fluorescence and useonly light scatter for measurement.

Flow cytometers can analyze several thousand particles every second in“real time” and can actively separate out and isolate particles havingspecified properties. They offer high-throughput automatedquantification, and separation, of the set parameters for a high numberof single cells during each analysis session. Flow cytomers can havemultiple lasers and fluorescence detectors, allowing multiple labels tobe used to more precisely specify a target population by theirphenotype. Thus, a flow cytometer, such as a multicolor flow cytometer,can be used to detect one or more vesicles with multiple fluorescentlabels or colors. In some embodiments, the flow cytometer can also sortor isolate different vesicle populations, such as by size or bydifferent markers.

The flow cytometer may have one or more lasers, such as 1, 2, 3, 4, 5,6, 7, 8, 9, 10 or more lasers. In some embodiments, the flow cytometercan detect more than one color or fluorescent label, such as at least 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20different colors or fluorescent labels. For example, the flow cytometercan have at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, or 20 fluorescence detectors.

Examples of commercially available flow cytometers that can be used todetect or analyze one or more vesicles, to sort or separate differentpopulations of vesicles, include, but are not limited to the MoFlo™ XDPCell Sorter (Beckman Coulter, Brea, Calif.), MoFlo™ Legacy Cell Sorter(Beckman Coulter, Brea, Calif.), BD FACSAria™ Cell Sorter (BDBiosciences, San Jose, Calif.), BD™ LSRII (BD Biosciences, San Jose,Calif.), and BD FACSCalibur™ (BD Biosciences, San Jose, Calif.). Use ofmulticolor or multi-fluor cytometers can be used in multiplex analysisof vesicles, as further described below. In some embodiments, the flowcytometer can sort, and thereby collect or sort more than one populationof vesicles based one or more characteristics. For example, twopopulations of vesicles differ in size, such that the vesicles withineach population have a similar size range and can be differentiallydetected or sorted. In another embodiment, two different populations ofvesicles are differentially labeled.

The data resulting from flow-cytometers can be plotted in 1 dimension toproduce histograms or seen in 2 dimensions as dot plots or in 3dimensions with newer software. The regions on these plots can besequentially separated by a series of subset extractions which aretermed gates. Specific gating protocols exist for diagnostic andclinical purposes especially in relation to hematology. The plots areoften made on logarithmic scales. Because different fluorescent dye'semission spectra overlap, signals at the detectors have to becompensated electronically as well as computationally. Fluorophores forlabeling biomarkers may include those described in Ormerod, FlowCytometry 2nd ed., Springer-Verlag, New York (1999), and in Nida et al.,Gynecologic Oncology 2005; 4 889-894 which is incorporated herein byreference.

Multiplexing

Multiplex experiments comprise experiments that can simultaneouslymeasure multiple analytes in a single assay. Vesicles and associatedbiomarkers can be assessed in a multiplex fashion. Different bindingagents can be used for multiplexing different circulating biomarkers,e.g., microRNA, protein, or vesicle populations. Different biomarkers,e.g., different vesicle populations, can be isolated or detected usingdifferent binding agents. Each population in a biological sample can belabeled with a different signaling label, such as a fluorophore, quantumdot, or radioactive label, such as described above. The label can bedirectly conjugated to a binding agent or indirectly used to detect abinding agent that binds a vesicle. The number of populations detectedin a multiplexing assay is dependent on the resolution capability of thelabels and the summation of signals, as more than two differentiallylabeled vesicle populations that bind two or more affinity elements canproduce summed signals.

Multiplexing of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 25, 50, 75 or 100 different circulating biomarkersmay be performed. For example, one population of vesicles specific to acell-of-origin can be assayed along with a second population of vesiclesspecific to a different cell-of-origin, where each population is labeledwith a different label. Alternatively, a population of vesicles with aparticular biomarker or biosignature can be assayed along with a secondpopulation of vesicles with a different biomarker or biosignature. Insome cases, hundreds or thousands of vesicles are assessed in a singleassay.

In one embodiment, multiplex analysis is performed by applying aplurality of vesicles comprising more than one population of vesicles toa plurality of substrates, such as beads. Each bead is coupled to one ormore capture agents. The plurality of beads is divided into subsets,where beads with the same capture agent or combination of capture agentsform a subset of beads, such that each subset of beads has a differentcapture agent or combination of capture agents than another subset ofbeads. The beads can then be used to capture vesicles that comprise acomponent that binds to the capture agent. The different subsets can beused to capture different populations of vesicles. The captured vesiclescan then be analyzed by detecting one or more biomarkers.

Flow cytometry can be used in combination with a particle-based or beadbased assay. Multiparametric immunoassays or other high throughputdetection assays using bead coatings with cognate ligands and reportermolecules with specific activities consistent with high sensitivityautomation can be used. For example, beads in each subset can bedifferentially labeled from another subset. In a particle based assaysystem, a binding agent or capture agent for a vesicle, such as acapture antibody, can be immobilized on addressable beads ormicrospheres. Each binding agent for each individual binding assay (suchas an immunoassay when the binding agent is an antibody) can be coupledto a distinct type of microsphere (i.e., microbead) and the bindingassay reaction takes place on the surface of the microspheres.Microspheres can be distinguished by different labels, for example, amicrosphere with a specific capture agent would have a differentsignaling label as compared to another microsphere with a differentcapture agent. For example, microspheres can be dyed with discretefluorescence intensities such that the fluorescence intensity of amicrosphere with a specific binding agent is different than that ofanother microsphere with a different binding agent. Biomarkers bound bydifferent capture agents can be differentially detected using differentlabels.

A microsphere can be labeled or dyed with at least 2 different labels ordyes. In some embodiments, the microsphere is labeled with at least 3,4, 5, 6, 7, 8, 9, or 10 different labels. Different microspheres in aplurality of microspheres can have more than one label or dye, whereinvarious subsets of the microspheres have various ratios and combinationsof the labels or dyes permitting detection of different microsphereswith different binding agents. For example, the various ratios andcombinations of labels and dyes can permit different fluorescentintensities. Alternatively, the various ratios and combinations maybeused to generate different detection patters to identify the bindingagent. The microspheres can be labeled or dyed externally or may haveintrinsic fluorescence or signaling labels. Beads can be loadedseparately with their appropriate binding agents and thus, differentvesicle populations can be isolated based on the different bindingagents on the differentially labeled microspheres to which the differentbinding agents are coupled.

In another embodiment, multiplex analysis can be performed using aplanar substrate, wherein the substrate comprises a plurality of captureagents. The plurality of capture agents can capture one or morepopulations of vesicles, and one or more biomarkers of the capturedvesicles detected. The planar substrate can be a microarray or othersubstrate as further described herein.

Binding Agents

A vesicle may be isolated or detected using a binding agent for a novelcomponent of a vesicle, such as an antibody for a novel antigen specificto a vesicle of interest. Novel antigens that are specific to a vesicleof interest may be isolated or identified using different test compoundsof known composition bound to a substrate, such as an array or aplurality of particles, which can allow a large amount ofchemical/structural space to be adequately sampled using only a smallfraction of the space. The novel antigen identified can also serve as abiomarker for the vesicle. For example, a novel antigen identified for acell-of-origin specific vesicle can be a useful biomarker.

The term “agent” or “reagent” as used in respect to contacting a samplecan mean any entity designed to bind, hybridize, associate with orotherwise detect or facilitate detection of a target molecule, includingtarget polypeptides, peptides, nucleic acid molecules, leptins, lipids,or any other biological entity that can be detected as described hereinor as known in the art. Examples of such agents/reagents are well knownin the art, and include but are not limited to universal or specificnucleic acid primers, nucleic acid probes, antibodies, aptamers,peptoid, peptide nucleic acid, locked nucleic acid, lectin, dendrimer,chemical compound, or other entities described herein or known in theart.

A binding agent can be identified by screening either a homogeneous orheterogeneous vesicle population against test compounds. Since thecomposition of each test compound on the substrate surface is known,this constitutes a screen for affinity elements. For example, a testcompound array comprises test compounds at specific locations on thesubstrate addressable locations, and can be used to identify one or morebinding agents for a vesicle. The test compounds can all be unrelated orrelated based on minor variations of a core sequence or structure. Thedifferent test compounds may include variants of a given test compound(such as polypeptide isoforms), test compounds that are structurally orcompositionally unrelated, or a combination thereof.

A test compound can be a peptoid, polysaccharide, organic compound,inorganic compound, polymer, lipids, nucleic acid, polypeptide,antibody, protein, polysaccharide, or other compound. The test compoundcan be natural or synthetic. The test compound can comprise or consistof linear or branched heteropolymeric compounds based on any of a numberof linkages or combinations of linkages (e.g., amide, ester, ether,thiol, radical additions, metal coordination, etc.), dendriticstructures, circular structures, cavity structures or other structureswith multiple nearby sites of attachment that serve as scaffolds uponwhich specific additions are made. These test compound can be spotted ona substrate or synthesized in situ, using standard methods in the art.In addition, the test compound can be spotted or synthesized in situ incombinations in order to detect useful interactions, such as cooperativebinding.

The test compound can be a polypeptide with known amino acid sequence,thus, detection of a test compound binding with a vesicle can lead toidentification of a polypeptide of known amino sequence that can be usedas a binding agent. For example, a homogenous population of vesicles canbe applied to a spotted array on a slide containing between a few and1,000,000 test polypeptides having a length of variable amino acids. Thepolypeptides can be attached to the surface through the C-terminus. Thesequence of the polypeptides can be generated randomly from 19 aminoacids, excluding cysteine. The binding reaction can include anon-specific competitor, such as excess bacterial proteins labeled withanother dye such that the specificity ratio for each polypeptide bindingtarget can be determined. The polypeptides with the highest specificityand binding can be selected. The identity of the polypeptide on eachspot is known, and thus can be readily identified. Once the novelantigens specific to the homogeneous vesicle population, such as acell-of-origin specific vesicle is identified, such cell-of-originspecific vesicles may subsequently be isolated using such antigens inmethods described hereafter.

An array can also be used for identifying an antibody as a binding agentfor a vesicle. Test antibodies can be attached to an array and screenedagainst a heterogeneous population of vesicles to identify antibodiesthat can be used to isolate or identify a vesicle. A homogeneouspopulation of vesicles such as cell-of-origin specific vesicles can alsobe screened with an antibody array. Other than identifying antibodies toisolate or detect a homogeneous population of vesicles, one or moreprotein biomarkers specific to the homogenous population can beidentified. Commercially available platforms with test antibodiespre-selected or custom selection of test antibodies attached to thearray can be used. For example, an antibody array from Full MoonBiosystems can be screened using prostate cancer cell derived vesiclesidentifying antibodies to Bcl-XL, ERCC1, Keratin 15, CD81/TAPA-1, CD9,Epithelial Specific Antigen (ESA), and Mast Cell Chymase as bindingagents, and the proteins identified can be used as biomarkers for thevesicles. The biomarker can be present or absent, underexpressed oroverexpressed, mutated, or modified in or on a vesicle and used incharacterizing a condition.

An antibody or synthetic antibody to be used as a binding agent can alsobe identified through a peptide array. Another method is the use ofsynthetic antibody generation through antibody phage display. M13bacteriophage libraries of antibodies (e.g. Fabs) are displayed on thesurfaces of phage particles as fusions to a coat protein. Each phageparticle displays a unique antibody and also encapsulates a vector thatcontains the encoding DNA. Highly diverse libraries can be constructedand represented as phage pools, which can be used in antibody selectionfor binding to immobilized antigens. Antigen-binding phages are retainedby the immobilized antigen, and the nonbinding phages are removed bywashing. The retained phage pool can be amplified by infection of anEscherichia coli host and the amplified pool can be used for additionalrounds of selection to eventually obtain a population that is dominatedby antigen-binding clones. At this stage, individual phase clones can beisolated and subjected to DNA sequencing to decode the sequences of thedisplayed antibodies. Through the use of phase display and other methodsknown in the art, high affinity designer antibodies for vesicles can begenerated.

Bead-based assays can also be used to identify novel binding agents toisolate or detect a vesicle. A test antibody or peptide can beconjugated to a particle. For example, a bead can be conjugated to anantibody or peptide and used to detect and quantify the proteinsexpressed on the surface of a population of vesicles in order todiscover and specifically select for novel antibodies that can targetvesicles from specific tissue or tumor types. Any molecule of organicorigin can be successfully conjugated to a polystyrene bead through useof a commercially available kit according to manufacturer'sinstructions. Each bead set can be colored a certain detectablewavelength and each can be linked to a known antibody or peptide whichcan be used to specifically measure which beads are linked to exosomalproteins matching the epitope of previously conjugated antibodies orpeptides. The beads can be dyed with discrete fluorescence intensitiessuch that each bead with a different intensity has a different bindingagent as described above.

For example, a purified vesicle preparation can be diluted in assaybuffer to an appropriate concentration according to empiricallydetermined dynamic range of assay. A sufficient volume of coupled beadscan be prepared and approximately 1 μl of the antibody-coupled beads canbe aliquoted into a well and adjusted to a final volume of approximately50 μl. Once the antibody-conjugated beads have been added to a vacuumcompatible plate, the beads can be washed to ensure proper bindingconditions. An appropriate volume of vesicle preparation can then beadded to each well being tested and the mixture incubated, such as for15-18 hours. A sufficient volume of detection antibodies using detectionantibody diluent solution can be prepared and incubated with the mixturefor 1 hour or for as long as necessary. The beads can then be washedbefore the addition of detection antibody (biotin expressing) mixturecomposed of streptavidin phycoereythin. The beads can then be washed andvacuum aspirated several times before analysis on a suspension arraysystem using software provided with an instrument. The identity ofantigens that can be used to selectively extract the vesicles can thenbe elucidated from the analysis.

Assays using imaging systems can be used to detect and quantify proteinsexpressed on the surface of a vesicle in order to discover andspecifically select for and enrich vesicles from specific tissue, cellor tumor types. Antibodies, peptides or cells conjugated to multiplewell multiplex carbon coated plates can be used. Simultaneousmeasurement of many analytes in a well can be achieved through the useof capture antibodies arrayed on the patterned carbon working surface.Analytes can then be detected with antibodies labeled with reagents inelectrode wells with an enhanced electro-chemiluminescent plate. Anymolecule of organic origin can be successfully conjugated to the carboncoated plate. Proteins expressed on the surface of vesicles can beidentified from this assay and can be used as targets to specificallyselect for and enrich vesicles from specific tissue or tumor types.

The binding agent can also be an aptamer, which refers to nucleic acidsthat can bond molecules other than their complementary sequence. Anaptamer typically contains 30-80 nucleic acids and can have a highaffinity towards a certain target molecule (K_(d)'s reported are between10⁻¹¹-10⁻⁶ mole/l). An aptamer for a target can be identified usingsystematic evolution of ligands by exponential enrichment (SELEX) (Tuerk& Gold, Science 249:505-510, 1990; Ellington & Szostak, Nature346:818-822, 1990), such as described in U.S. Pat. Nos. 5,270,163,6,482,594, 6,291,184, 6,376,190 and U.S. Pat. No. 6,458,539. A libraryof nucleic acids can be contacted with a target vesicle, and thosenucleic acids specifically bound to the target are partitioned from theremainder of nucleic acids in the library which do not specifically bindthe target. The partitioned nucleic acids are amplified to yield aligand-enriched pool. Multiple cycles of binding, partitioning, andamplifying (i.e., selection) result in identification of one or moreaptamers with the desired activity. Another method for identifying anaptamer to isolate vesicles is described in U.S. Pat. No. 6,376,190,which describes increasing or decreasing frequency of nucleic acids in alibrary by their binding to a chemically synthesized peptide. Modifiedmethods, such as Laser SELEX or deSELEX as described in U.S. PatentPublication No. 20090264508 can also be used.

The term “specific” as used herein in regards to a binding agent canmean that an agent has a greater affinity for its target than othertargets, typically with a much great affinity, but does not require thatthe binding agent is absolutely specific for its target.

Microfluidics

The methods for isolating or identifying vesicles can be used incombination with microfluidic devices. The methods of isolating ordetecting a vesicle, such as described herein, can be performed using amicrofluidic device. Microfluidic devices, which may also be referred toas “lab-on-a-chip” systems, biomedical micro-electro-mechanical systems(bioMEMs), or multicomponent integrated systems, can be used forisolating and analyzing a vesicle. Such systems miniaturize andcompartmentalize processes that allow for binding of vesicles, detectionof biosignatures, and other processes.

A microfluidic device can also be used for isolation of a vesiclethrough size differential or affinity selection. For example, amicrofluidic device can use one more channels for isolating a vesiclefrom a biological sample based on size or by using one or more bindingagents for isolating a vesicle from a biological sample. A biologicalsample can be introduced into one or more microfluidic channels, whichselectively allows the passage of a vesicle. The selection can be basedon a property of the vesicle, such as the size, shape, deformability, orbiosignature of the vesicle.

In one embodiment, a heterogeneous population of vesicles can beintroduced into a microfluidic device, and one or more differenthomogeneous populations of vesicles can be obtained. For example,different channels can have different size selections or binding agentsto select for different vesicle populations. Thus, a microfluidic devicecan isolate a plurality of vesicles wherein at least a subset of theplurality of vesicles comprises a different biosignature from anothersubset of the plurality of vesicles. For example, the microfluidicdevice can isolate at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,40, 50, 60, 70, 80, 90, or 100 different subsets of vesicles, whereineach subset of vesicles comprises a different biosignature.

In some embodiments, the microfluidic device can comprise one or morechannels that permit further enrichment or selection of a vesicle. Apopulation of vesicles that has been enriched after passage through afirst channel can be introduced into a second channel, which allows thepassage of the desired vesicle or vesicle population to be furtherenriched, such as through one or more binding agents present in thesecond channel.

Array-based assays and bead-based assays can be used with microfluidicdevice. For example, the binding agent can be coupled to beads and thebinding reaction between the beads and vesicle can be performed in amicrofluidic device. Multiplexing can also be performed using amicrofluidic device. Different compartments can comprise differentbinding agents for different populations of vesicles, where eachpopulation is of a different cell-of-origin specific vesicle population.In one embodiment, each population has a different biosignature. Thehybridization reaction between the microsphere and vesicle can beperformed in a microfluidic device and the reaction mixture can bedelivered to a detection device. The detection device, such as a dual ormultiple laser detection system can be part of the microfluidic systemand can use a laser to identify each bead or microsphere by itscolor-coding, and another laser can detect the hybridization signalassociated with each bead.

Any appropriate microfluidic device can be used in the methods of theinvention. Examples of microfluidic devices that may be used, or adaptedfor use with vesicles, include but are not limited to those described inU.S. Pat. Nos. 7,591,936, 7,581,429, 7,579,136, 7,575,722, 7,568,399,7,552,741, 7,544,506, 7,541,578, 7,518,726, 7,488,596, 7,485,214,7,467,928, 7,452,713, 7,452,509, 7,449,096, 7,431,887, 7,422,725,7,422,669, 7,419,822, 7,419,639, 7,413,709, 7,411,184, 7,402,229,7,390,463, 7,381,471, 7,357,864, 7,351,592, 7,351,380, 7,338,637,7,329,391, 7,323,140, 7,261,824, 7,258,837, 7,253,003, 7,238,324,7,238,255, 7,233,865, 7,229,538, 7,201,881, 7,195,986, 7,189,581,7,189,580, 7,189,368, 7,141,978, 7,138,062, 7,135,147, 7,125,711,7,118,910, 7,118,661, 7,640,947, 7,666,361, 7,704,735; and InternationalPatent Publication WO 2010/072410; each of which patents or applicationsare incorporated herein by reference in their entirety. Another examplefor use with methods disclosed herein is described in Chen et al.,“Microfluidic isolation and transcriptome analysis of serum vesicles,”Lab on a Chip, Dec. 8, 2009 DOI: 10.1039/b916199f.

Other microfluidic devices for use with the invention include devicescomprising elastomeric layers, valves and pumps, including withoutlimitation those disclosed in U.S. Pat. Nos. 5,376,252, 6,408,878,6,645,432, 6,719,868, 6,793,753, 6,899,137, 6,929,030, 7,040,338,7,118,910, 7,144,616, 7,216,671, 7,250,128, 7,494,555, 7,501,245,7,601,270, 7,691,333, 7,754,010, 7,837,946; U.S. Patent Application Nos.2003/0061687, 2005/0084421, 2005/0112882, 2005/0129581, 2005/0145496,2005/0201901, 2005/0214173, 2005/0252773, 2006/0006067; and EP PatentNos. 0527905 and 1065378; each of which application is hereinincorporated by reference. In some instances, much or all of the devicesare composed of elastomeric material. Certain devices are designed toconduct thermal cycling reactions (e.g., PCR) with devices that includeone or more elastomeric valves to regulate solution flow through thedevice. The devices can comprise arrays of reaction sites therebyallowing a plurality of reactions to be performed. Thus, the devices canbe used to assess circulating microRNAs in a multiplex fashion,including microRNAs isolated from vesicles. In an embodiment, themicrofluidic device comprises (a) a first plurality of flow channelsformed in an elastomeric substrate; (b) a second plurality of flowchannels formed in the elastomeric substrate that intersect the firstplurality of flow channels to define an array of reaction sites, eachreaction site located at an intersection of one of the first and secondflow channels; (c) a plurality of isolation valves disposed along thefirst and second plurality of flow channels and spaced between thereaction sites that can be actuated to isolate a solution within each ofthe reaction sites from solutions at other reaction sites, wherein theisolation valves comprise one or more control channels that each overlayand intersect one or more of the flow channels; and (d) means forsimultaneously actuating the valves for isolating the reaction sitesfrom each other. Various modifications to the basic structure of thedevice are envisioned within the scope of the invention. MicroRNAs canbe detected in each of the reaction sites by using PCR methods. Forexample, the method can comprise the steps of the steps of: (i)providing a microfluidic device, the microfluidic device comprising: afirst fluidic channel having a first end and a second end in fluidcommunication with each other through the channel; a plurality of flowchannels, each flow channel terminating at a terminal wall; wherein eachflow channel branches from and is in fluid communication with the firstfluidic channel, wherein an aqueous fluid that enters one of the flowchannels from the first fluidic channel can flow out of the flow channelonly through the first fluidic channel; and, an inlet in fluidcommunication with the first fluidic channel, the inlet for introducinga sample fluid; wherein each flow channel is associated with a valvethat when closed isolates one end of the flow channel from the firstfluidic channel, whereby an isolated reaction site is formed between thevalve and the terminal wall; a control channel; wherein each the valveis a deflectable membrane which is deflected into the flow channelassociated with the valve when an actuating force is applied to thecontrol channel, thereby closing the valve; and wherein when theactuating force is applied to the control channel a valve in each of theflow channels is closed, so as to produce the isolated reaction site ineach flow channel; (ii) introducing the sample fluid into the inlet, thesample fluid filling the flow channels; (iii) actuating the valve toseparate the sample fluid into the separate portions within the flowchannels; (iv) amplifying the nucleic acid in the sample fluid; (v)analyzing the portions of the sample fluid to determine whether theamplifying produced the reaction. The sample fluid can contain anamplifiable nucleic acid target, e.g., a microRNA, and the conditionscan be polymerase chain reaction (PCR) conditions, so that the reactionresults in a PCR product being formed.

In an embodiment, the PCR used to detect microRNA is digital PCR, whichis described by Brown, et al., U.S. Pat. No. 6,143,496, titled “Methodof sampling, amplifying and quantifying segment of nucleic acid,polymerase chain reaction assembly having nanoliter-sized chambers andmethods of filling chambers”, and by Vogelstein, et al, U.S. Pat. No.6,446,706, titled “Digital PCR”, both of which are hereby incorporatedby reference in their entirety. In digital PCR, a sample is partitionedso that individual nucleic acid molecules within the sample arelocalized and concentrated within many separate regions, such as thereaction sites of the microfluidic device described above. Thepartitioning of the sample allows one to count the molecules byestimating according to Poisson. As a result, each part will contain “0”or “1” molecules, or a negative or positive reaction, respectively.After PCR amplification, nucleic acids may be quantified by counting theregions that contain PCR end-product, positive reactions. Inconventional PCR, starting copy number is proportional to the number ofPCR amplification cycles. Digital PCR, however, is not dependent on thenumber of amplification cycles to determine the initial sample amount,eliminating the reliance on uncertain exponential data to quantifytarget nucleic acids and providing absolute quantification. Thus, themethod can provide a sensitive approach to detecting microRNAs in asample.

In one embodiment, a microfluidic device for isolating or detecting avesicle comprises a channel of less than about 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 35, 40, 45, 50, 55, of 60 mm in width, or between about2-60, 3-50, 3-40, 3-30, 3-20, or 4-20 mm in width. The microchannel canhave a depth of less than about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 45, 50, 55, 60, 65 or 70 μm, or between about 10-70, 10-40,15-35, or 20-30 μm. Furthermore, the microchannel can have a length ofless than about 1, 2, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9,9.5 or 10 cm. The microfluidic device can have grooves on its ceilingthat are less than about 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,52, 53, 54, 55, 56, 57, 58, 59, 6, 65, 70, 75, or 80 μm wide, or betweenabout 40-80, 40-70, 40-60 or 45-55 μm wide. The grooves can be less thanabout 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 25, 30, 35, 40, 45, or 50 μm deep, such as between about 1-50, 5-40,5-30, 3-20 or 5-15 μm.

The microfluidic device can have one or more binding agents attached toa surface in a channel, or present in a channel. For example, themicrochannel can have one or more capture agents, such as a captureagent for EpCam, CD9, PCSA, CD63, CD81, PSMA, B7H3, PSCA, ICAM, STEAP,and EGFR. In one embodiment, a microchannel surface is treated withavidin and a capture agent, such as an antibody, that is biotinylatedcan be injected into the channel to bind the avidin. In otherembodiments, the capture agents are present in chambers or othercomponents of a microfluidic device. The capture agents can also beattached to beads that can be manipulated to move through themicrofluidic channels. In one embodiment, the capture agents areattached to magnetic beads. The beads can be manipulated using magnets.

A biological sample can be flowed into the microfluidic device, or amicrochannel, at rates such as at least about 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50 μlper minute, such as between about 1-50, 5-40, 5-30, 3-20 or 5-15 μl perminute. One or more vesicles can be captured and directly detected inthe microfluidic device. Alternatively, the captured vesicle may bereleased and exit the microfluidic device prior to analysis. In anotherembodiment, one or more captured vesicles are lysed in the microchanneland the lysate can be analyzed, e.g., to examine payload within thevesicles. Lysis buffer can be flowed through the channel and lyse thecaptured vesicles. For example, the lysis buffer can be flowed into thedevice or microchannel at rates such as at least about a, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29,30, 35, 40, 45, or 50 μl per minute, such as between about 1-50, 5-40,10-30, 5-30 or 10-35 μl per minute. The lysate can be collected andanalyzed, such as performing RT-PCR, PCR, mass spectrometry, Westernblotting, or other assays, to detect one or more biomarkers of thevesicle.

The various isolation and detection systems described herein can be usedto isolate or detect circulating biomarkers such as vesicles that areinformative for diagnosis, prognosis, disease stratification,theranosis, prediction of responder/non-responder status, diseasemonitoring, treatment monitoring and the like as related to suchdiseases and disorders. Combinations of the isolation techniques arewithin the scope of the invention. In a non-limiting example, a samplecan be run through a chromatography column to isolate vesicles based ona property such as size of electrophoretic motility, and the vesiclescan then be passed through a microfluidic device. Binding agents can beused before, during or after these steps.

Cell and Disease-Specific Vesicles

The bindings agent disclosed herein can be used to isolate or detect avesicle, such as a cell-of-origin vesicle or vesicle with a specificbiosignature. The binding agent can be used to isolate or detect aheterogeneous population of vesicles from a sample or can be used toisolate or detect a homogeneous population of vesicles, such ascell-of-origin specific vesicles with specific biosignatures, from aheterogeneous population of vesicles.

A homogeneous population of vesicles, such as cell-of-origin specificvesicles, can be analyzed and used to characterize a phenotype for asubject. Cell-of-origin specific vesicles are esicles derived fromspecific cell types, which can include, but are not limited to, cells ofa specific tissue, cells from a specific tumor of interest or a diseasedtissue of interest, circulating tumor cells, or cells of maternal orfetal origin. The vesicles may be derived from tumor cells or lung,pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin,colorectal, breast, prostate, brain, esophagus, liver, placenta, orfetal cells. The isolated vesicle can also be from a particular sampletype, such as urinary vesicle.

A cell-of-origin specific vesicle from a biological sample can beisolated using one or more binding agents that are specific to acell-of-origin. Vesicles for analysis of a disease or condition can beisolated using one or more binding agent specific for biomarkers forthat disease or condition.

A vesicle can be concentrated prior to isolation or detection of acell-of-origin specific vesicle, such as through centrifugation,chromatography, or filtration, as described above, to produce aheterogeneous population of vesicles prior to isolation ofcell-of-origin specific vesicles. Alternatively, the vesicle is notconcentrated, or the biological sample is not enriched for a vesicle,prior to isolation of a cell-of-origin vesicle.

FIG. 1B illustrates a flowchart which depicts one method 6100B forisolating or identifying a cell-of-origin specific vesicle. First, abiological sample is obtained from a subject in step 6102. The samplecan be obtained from a third party or from the same party performing theanalysis. Next, cell-of-origin specific vesicles are isolated from thebiological sample in step 6104. The isolated cell-of-origin specificvesicles are then analyzed in step 6106 and a biomarker or biosignaturefor a particular phenotype is identified in step 6108. The method may beused for a number of phenotypes. In some embodiments, prior to step6104, vesicles are concentrated or isolated from a biological sample toproduce a homogeneous population of vesicles. For example, aheterogeneous population of vesicles may be isolated usingcentrifugation, chromatography, filtration, or other methods asdescribed above, prior to use of one or more binding agents specific forisolating or identifying vesicles derived from specific cell types.

A cell-of-origin specific vesicle can be isolated from a biologicalsample of a subject by employing one or more binding agents that bindwith high specificity to the cell-of-origin specific vesicle. In someinstances, a single binding agent can be employed to isolate acell-of-origin specific vesicle. In other instances, a combination ofbinding agents may be employed to isolate a cell-of-origin specificvesicle. For example, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 25, 50, 75, or 100 different binding agentsmay be used to isolate a cell-of-origin vesicle. Therefore, a vesiclepopulation (e.g., vesicles having the same binding agent profile) can beidentified by using a single or a plurality of binding agents.

One or more binding agents can be selected based on their specificityfor a target antigen(s) that is specific to a cell-of-origin, e.g., acell-of-origin that is related to a tumor, autoimmune disease,cardiovascular disease, neurological disease, infection or other diseaseor disorder. The cell-of-origin can be from a cell that is informativefor a diagnosis, prognosis, disease stratification, theranosis,prediction of responder/non-responder status, disease monitoring,treatment monitoring and the like as related to such diseases anddisorders. The cell-of-origin can also be from a cell useful to discoverbiomarkers for use thereto. Non-limiting examples of antigens which maybe used singularly, or in combination, to isolate a cell-of-originspecific vesicle, disease specific vesicle, or tumor specific vesicle,are shown in FIG. 1 of International Patent Application Serial No.PCT/US2011/031479, entitled “Circulating Biomarkers for Disease” andfiled Apr. 6, 2011, which application is incorporated by reference inits entirety herein, and are also described herein. The antigen cancomprise membrane bound antigens which are accessible to binding agents.The antigen can be a biomarker related to characterizing a phenotype.

One of skill will appreciate that any applicable antigen that can beused to isolate an informative vesicle is contemplated by the invention.Binding agents, e.g., antibodies, aptamers and lectins, can be chosenthat recognize surface antigens and/or fragments thereof, as outlinedherein. The binding agents can recognize antigens specific to thedesired cell type or location and/or recognize biomarkers associatedwith the desired cells. The cells can be, e.g., tumor cells, otherdiseased cells, cells that serve as markers of disease such as activatedimmune cells, etc. One of skill will appreciate that binding agents forany cells of interest can be useful for isolating vesicles associatedwith those cells. One of skill will further appreciate that the bindingagents disclosed herein can be used for detecting vesicles of interest.As a non-limiting example, a binding agent to a vesicle biomarker can belabeled directly or indirectly in order to detect vesicles bound by oneof more of the same or different binding agents.

A number of targets for binding agents useful for binding to vesiclesassociated with cancer, autoimmune diseases, cardiovascular diseases,neurological diseases, infection or other disease or disorders arepresented in Table 4. A vesicle derived from a cell associated with oneof the listed disorders can be characterized using one of the antigensin the table. The binding agent, e.g., an antibody or aptamer, canrecognize an epitope of the listed antigens, a fragment thereof, orbinding agents can be used against any appropriate combination. Otherantigens associated with the disease or disorder can be recognized aswell in order to characterize the vesicle. One of skill will appreciatethat any applicable antigen that can be used to assess an informativevesicle is contemplated by the invention for isolation, capture ordetection in order to characterize a vesicle.

TABLE 4 Illustrative Antigens for Use in Characterizing Various Diseasesand Disorders Disease or disorder Target Breast cancer, e.g., glandularor stromal cells BCA-225, hsp70, MART1, ER, VEGFA, Class III b- tubulin,HER2/neu (for Her2+ breast cancer), GPR30, ErbB4 (JM) isoform, MPR8,MISIIR Breast cancer CD9, MIS Rii, ER, CD63, MUC1, HER3, STAT3, VEGFA,BCA, CA125, CD24, EPCAM, ERB B4 Breast cancer BCA-225, hsp70, MART1, ER,VEGFA, Class III b- tubulin, HER2/neu (e.g., for Her2+ breast cancer),GPR30, ErbB4 (JM) isoform, MPR8, MISIIR, CD9, EphA2, EGFR, B7H3, PSM,PCSA, CD63, STEAP, CD81, ICAM1, A33, DR3, CD66e, MFG-E8, TROP-2,Mammaglobin, Hepsin, NPGP/NPFF2, PSCA, 5T4, NGAL, EpCam, neurokininreceptor-1 (NK-1 or NK- 1R), NK-2, Pai-1, CD45, CD10, HER2/ERBB2, AGTR1,NPY1R, MUC1, ESA, CD133, GPR30, BCA225, CD24, CA15.3 (MUC1 secreted),CA27.29 (MUC1 secreted), NMDAR1, NMDAR2, MAGEA, CTAG1B, NY-ESO-1, SPB,SPC, NSE, PGP9.5, a progesterone receptor (PR) or its isoform (PR(A) orPR(B)), P2RX7, NDUFB7, NSE, GAL3, osteopontin, CHI3L1, IC3b, mesothelin,SPA, AQP5, GPCR, hCEA-CAM, PTP IA-2, CABYR, TMEM211, ADAM28, UNC93A,MUC17, MUC2, IL10R-beta, BCMA, HVEM/TNFRSF14, Trappin-2 Elafin, ST2/IL1R4, TNFRF14, CEACAM1, TPA1, LAMP, WF, WH1000, PECAM, BSA, TNF Breastcancer CD10, NPGP/NPFF2, HER2/ERBB2, AGTR1, NPY1R, neurokinin receptor-1(NK-1 or NK-1R), NK- 2, MUC1, ESA, CD133, GPR30, BCA225, CD24, CA15.3(MUC1 secreted), CA27.29 (MUC1 secreted), NMDAR1, NMDAR2, MAGEA, CTAG1B,NY-ESO-1 Breast cancer SPB, SPC, NSE, PGP9.5, CD9, P2RX7, NDUFB7, NSE,GAL3, osteopontin, CHI3L1, EGFR, B7H3, IC3b, MUC1, mesothelin, SPA,PCSA, CD63, STEAP, AQP5, CD81, DR3, PSM, GPCR, EphA2, hCEA- CAM, PTPIA-2, CABYR, TMEM211, ADAM28, UNC93A, A33, CD24, CD10, NGAL, EpCam,MUC17, TROP-2, MUC2, IL10R-beta, BCMA, HVEM/TNFRSF14, Trappin-2 Elafin,ST2/IL1 R4, TNFRF14, CEACAM1, TPA1, LAMP, WF, WH1000, PECAM, BSA, TNFRBreast cancer BRCA, MUC-1, MUC 16, CD24, ErbB4, ErbB2 (HER2), ErbB3,HSP70, Mammaglobin, PR, PR(B), VEGFA Ovarian Cancer CA125, VEGFR2, HER2,MISIIR, VEGFA, CD24, c- reactive protein EGFR, EGFRvIII, apolipoproteinAI, apolipoprotein CIII, myoglobin, tenascin C, MSH6, claudin-3,claudin-4, caveolin-1, coagulation factor III, CD9, CD36, CD37, CD53,CD63, CD81, CD136, CD147, Hsp70, Hsp90, Rab13, Desmocollin-1, EMP- 2,CK7, CK20, GCDF15, CD82, Rab-5b, Annexin V, MFG-E8, HLA-DR, CD95 LungCancer CYFRA21-1, TPA-M, TPS, CEA, SCC-Ag, XAGE- 1b, HLA Class 1,TA-MUC1, KRAS, hENT1, kinin B1 receptor, kinin B2 receptor, TSC403,HTI56, DC- LAMP Lung Cancer SPB, SPC, PSP9.5, NDUFB7, gal3-b2c10, iC3b,MUC1, GPCR, CABYR and muc17 Colorectal Cancer CEA, MUC2, GPA33, CEACAM5,ENFB1, CCSA-3, CCSA-4, ADAM10, CD44, NG2, ephrin B1, plakoglobin,galectin 4, RACK1, tetraspanin-8, FASL, A33, CEA, EGFR, dipeptidase 1,PTEN, Na(+)- dependent glucose transporter, UDP- glucuronosyltransferase1A, TMEM211, CD24 Prostate Cancer PSA, TMPRSS2, FASLG, TNFSF10, PSMA,NGEP, I1-7RI, CSCR4, CysLT1R, TRPM8, Kv1.3, TRPV6, TRPM8, PSGR, MISIIR,galectin-3, PCA3, TMPRSS2:ERG Brain Cancer PRMT8, BDNF, EGFR, DPPX, Elk,Densin-180, BAI2, BAI3 Blood Cancer (hematological malignancy) CD44,CD58, CD31, CD11a, CD49d, GARP, BTS, Raftlin Melanoma DUSP1, TYRP1,SILV, MLANA, MCAM, CD63, Alix, hsp70, meosin, p120 catenin, PGRL,syntaxin binding protein 1 & 2, caveolin Liver Cancer (hepatocellularcarcinoma) HBxAg, HBsAg, NLT Cervical Cancer MCT-1, MCT-2, MCT-4Endometrial Cancer Alpha V Beta 6 integrin Psoriasis flt-1, VPFreceptors, kdr Autoimmune Disease Tim-2 Irritable Bowel Disease (IBD orSyndrome (IBS) IL-16, IL-1beta, IL-12, TNF-alpha, interferon-gamma,IL-6, Rantes, II-12, MCP-1, 5HT Diabetes, e.g., pancreatic cells IL-6,CRP, RBP4 Barrett's Esophagus p53, MUC1, MUC6 Fibromyalgia neopterin,gp130 Benign Prostatic Hyperplasia (BPH) KIA1, intact fibronectinMultiple Sclerosis B7, B7-2, CD-95 (fas), Apo-1/Fas Parkinson's DiseasePARK2, ceruloplasmin, VDBP, tau, DJ-1 Rheumatic Disease Citrulinatedfibrin a-chain, CD5 antigen-like fibrinogen fragment D, CD5 antigen-likefibrinogen fragment B, TNF alpha Alzheimer's Disease APP695, APP751 orAPP770, BACE1, cystatin C, amyloid β, T-tau, complement factor H,alpha-2- macroglobulin Head and Neck Cancer EGFR, EphB4, Ephrin B2Gastrointestinal Stromal Tumor (GIST) c-kit PDGFRA, NHE-3 Renal CellCarcinoma c PDGFRA, VEGF, HIF 1 alpha Schizophrenia ATP5B, ATP5H,ATP6V1B, DNM1 Peripheral Neuropathic Pain OX42, ED9 Chronic NeuropathicPain chemokine receptor (CCR2/4) Prion Disease PrPSc, 14-3-3 zeta,S-100, AQP4 Stroke S-100, neuron specific enolase, PARK7, NDKA, ApoC-I,ApoC-III, SAA or AT-III fragment, Lp- PLA2, hs-CRP CardiovascularDisease FATP6 Esophageal Cancer CaSR Tuberculosis antigen 60, HSP,Lipoarabinomannan, Sulfolipid, antigen of acylated trehalose family,DAT, TAT, Trehalose 6,6-dimycolate (cord-factor) antigen HIV gp41, gp120Autism VIP, PACAP, CGRP, NT3 Asthma YKL-40, S-nitrosothiols, SSCA2, PAI,amphiregulin, periostin Lupus TNFR Cirrhosis NLT, HBsAg Influenzahemagglutinin, neurominidase Vulnerable Plaque Alpha v. Beta 3 integrin,MMP9

The foregoing Table 4, as well as other biomarker lists disclosed hereare illustrative, and Applicants contemplate incorporating variousbiomarkers disclosed across different disease states or conditions. Forexample, method of the invention may use various biomarkers acrossdifferent diseases or conditions, where the biomarkers are useful forproviding a diagnostic, prognostic or theranostic signature. In oneembodiment, angiogenic, inflammatory or immune-associated antigens (orbiomarkers) disclosed herein or know in the art can be used in methodsof the invention to screen a biological sample in identification of abiosignature. Indeed, the flexibility of Applicants' multiplex approachto assessing microvesicle populations facilitates assessing variousmarkers (and in some instances overlapping markers) for differentconditions or diseases whose etiology necessarily may share certaincellular and biological mechanisms, e.g., different cancers implicatingbiomarkers for angiogenesis, or immune response regulation ormodulation. The combination of such overlapping biomarkers with tissueor cell-specific biomarkers, along with microvesicle-associatedbiomarkers provides a powerful series of tools for practicing themethods and compositions of the invention.

A cell-of-origin specific vesicle may be isolated using novel bindingagents, using methods as described herein. Furthermore, a cell-of-originspecific vesicle can also be isolated from a biological sample usingisolation methods based on cellular binding partners or binding agentsof such vesicles. Such cellular binding partners can include but are notlimited to peptides, proteins, RNA, DNA, apatmers, cells orserum-associated proteins that only bind to such vesicles when one ormore specific biomarkers are present. Isolation or detection of acell-of-origin specific vesicle can be carried out with a single bindingpartner or binding agent, or a combination of binding partners orbinding agents whose singular application or combined applicationresults in cell-of-origin specific isolation or detection. Non-limitingexamples of such binding agents are provided in FIG. 2 of InternationalPatent Application Serial No. PCT/US2011/031479, entitled “CirculatingBiomarkers for Disease” and filed Apr. 6, 2011, which application isincorporated by reference in its entirety herein. For example, a vesiclefor characterizing breast cancer can be isolated with one or morebinding agents including, but not limited to, estrogen, progesterone,trastuzumab, CCND1, MYC PNA, IGF-1 PNA, MYC PNA, SC4 aptamer (Ku), All-7aptamer (ERB2), Galectin-3, mucin-type O-glycans, L-PHA, Galectin-9, orany combination thereof.

A binding agent may also be used for isolating or detecting acell-of-origin specific vesicle based on: i) the presence of antigensspecific for cell-of-origin specific vesicles; ii) the absence ofmarkers specific for cell-of-origin specific vesicles; or iii)expression levels of biomarkers specific for cell-of-origin specificvesicles. A heterogeneous population of vesicles can be applied to asurface coated with specific binding agents designed to rule out oridentify the cell-of-origin characteristics of the vesicles. Variousbinding agents, such as antibodies, can be arrayed on a solid surface orsubstrate and the heterogeneous population of vesicles is allowed tocontact the solid surface or substrate for a sufficient time to allowinteractions to take place. Specific binding or non-binding to givenantibody locations on the array surface or substrate can then serve toidentify antigen specific characteristics of the vesicle population thatare specific to a given cell-of-origin. That is, binding events cansignal the presence of a vesicle having an antigen recognized by thebound antibody. Conversely, lack of binding events can signal theabsence of vesicles having an antigen recognized by the bound antibody.

A cell-of-origin specific vesicle can be enriched or isolated using oneor more binding agents using a magnetic capture method, fluorescenceactivated cell sorting (FACS) or laser cytometry as described above.Magnetic capture methods can include, but are not limited to, the use ofmagnetically activated cell sorter (MACS) microbeads or magneticcolumns. Examples of immunoaffinity and magnetic particle methods thatcan be used are described in U.S. Pat. No. 4,551,435, 4,795,698,4,925,788, 5,108,933, 5,186,827, 5,200,084 or 5,158,871. Acell-of-origin specific vesicle can also be isolated following thegeneral methods described in U.S. Pat. No. 7,399,632, by usingcombination of antigens specific to a vesicle.

Any other appropriate method for isolating or otherwise enriching thecell-of-origin specific vesicles with respect to a biological sample mayalso be used in combination with the present invention. For example,size exclusion chromatography such as gel permeation columns,centrifugation or density gradient centrifugation, and filtrationmethods can be used in combination with the antigen selection methodsdescribed herein. The cell-of-origin specific vesicles may also beisolated following the methods described in Koga et al., AnticancerResearch, 25:3703-3708 (2005), Taylor et al., Gynecologic Oncology,110:13-21 (2008), Nanjee et al., Clin Chem, 2000; 46:207-223 or U.S.Pat. No. 7,232,653.

Vesicles can be isolated and/or detected to provide diagnosis,prognosis, disease stratification, theranosis, prediction ofresponder/non-responder status, disease monitoring, treatment monitoringand the like. In one embodiment, vesicles are isolated from cells havinga disease or disorder, e.g., cells derived from a tumor or malignantgrowth, a site of autoimmune disease, cardiovascular disease,neurological disease, or infection. In some embodiments, the isolatedvesicles are derived from cells related to such diseases and disorders,e.g., immune cells that play a role in the etiology of the disease andwhose analysis is informative for a diagnosis, prognosis, diseasestratification, theranosis, prediction of responder/non-responderstatus, disease monitoring, treatment monitoring and the like as relatesto such diseases and disorders. The vesicles are further useful todiscover novel biomarkers. By identifying biomarkers associated withvesicles, isolated vesicles can be assessed for characterizing aphenotype as described herein.

In some embodiments, methods of the invention are directed tocharacterizing presence of a cancer or likelihood of a cancer occurringin an individual by assessing one or more microvesicle populationpresent in a biological sample from an individual. Microvesicles can beisolated using one or more processes disclosed herein or practiced inthe art.

Such microvesicles populations can each separately or collectivelyprovide a disease phenotype characterization for the individual bycomparing the biomarker profile, or biosignature, for the microvesiclepopulation(s) with a reference sample to provide a diagnostic,prognostic or theranostic characterization for the test sample.

The vesicle population(s) can be assessed from various biologicalsamples and bodily fluids such as disclosed herein.

Biomarker Assessment

In an aspect of the invention, a phenotype of a subject is characterizedby analyzing a biological sample and determining the presence, level,amount, or concentration of one or more populations of circulatingbiomarkers in the sample, e.g., circulating vesicles, proteins ornucleic acids. In embodiments, characterization includes determiningwhether the circulating biomarkers in the sample are altered as comparedto a reference, which can also be referred to a standard or a control.An alteration can include any measurable difference between the sampleand the reference, including without limitation an absolute presence orabsence, a quantitative level, a relative level compared to a reference,e.g., the level of all vesicles present, the level of a housekeepingmarker, and/or the level of a spiked-in marker, an elevated level, adecreased level, overexpression, underexpression, differentialexpression, a mutation or other altered sequence, a modification(glycosylation, phosphorylation, epigenetic change) and the like. Insome embodiments, circulating biomarkers are purified or concentratedfrom a sample prior to determining their amount. Unless otherwisespecified, “purified” or “isolated” as used herein refer to partial orcomplete purification or isolation. In other embodiments, circulatingbiomarkers are directly assessed from a sample, without priorpurification or concentration. Circulating vesicles can becell-of-origin specific vesicles or vesicles with a specificbiosignature. A biosignature includes specific pattern of biomarkers,e.g., patterns of biomarkers indicative of a phenotype that is desirableto detect, such as a disease phenotype. The biosignature can compriseone or more circulating biomarkers. A biosignature can be used whencharacterizing a phenotype, such as a diagnosis, prognosis, theranosis,or prediction of responder/non-responder status. In some embodiments,the biosignature is used to determine a physiological or biologicalstate, such as pregnancy or the stage of pregnancy. The biosignature canalso be used to determine treatment efficacy, stage of a disease orcondition, or progression of a disease or condition. For example, theamount of one or more vesicles can be proportional or inverselyproportional to an increase in disease stage or progression. Thedetected amount of vesicles can also be used to monitor progression of adisease or condition or to monitor a subject's response to a treatment.

The circulating biomarkers can be evaluated by comparing the level ofcirculating biomarkers with a reference level or value. The referencevalue can be particular to physical or temporal endpoint. For example,the reference value can be from the same subject from whom a sample isassessed, or the reference value can be from a representative populationof samples (e.g., samples from normal subjects not exhibiting a symptomof disease). Therefore, a reference value can provide a thresholdmeasurement which is compared to a subject sample's readout for abiosignature assayed in a given sample. Such reference values may be setaccording to data pooled from groups of sample corresponding to aparticular cohort, including but not limited to age (e.g., newborns,infants, adolescents, young, middle-aged adults, seniors and adults ofvaried ages), racial/ethnic groups, normal versus diseased subjects,smoker v. non-smoker, subject receiving therapy versus untreatedsubject, different time points of treatment for a particular individualor group of subjects similarly diagnosed or treated or combinationsthereof. Furthermore, by determining a biosignature at differenttimepoints of treatment for a particular individual, the individual'sresponse to the treatment or progression of a disease or condition forwhich the individual is being treated for, can be monitored.

A reference value may be based on samples assessed from the same subjectso to provide individualized tracking. In some embodiments, frequenttesting of a biosignature in samples from a subject provides bettercomparisons to the reference values previously established for thatsubject. Such time course measurements are used to allow a physician tomore accurately assess the subject's disease stage or progression andtherefore inform a better decision for treatment. In some cases, thevariance of a biosignature is reduced when comparing a subject's ownbiosignature over time, thus allowing an individualized threshold to bedefined for the subject, e.g., a threshold at which a diagnosis is made.Temporal intrasubject variation allows each individual to serve as theirown longitudinal control for optimum analysis of disease orphysiological state. As an illustrative example, consider that the levelof vesicles derived from prostate cells is measured in a subject's bloodover time. A spike in the level of prostate-derived vesicles in thesubject's blood can indicate hyperproliferation of prostate cells, e.g.,due to prostate cancer.

Reference values can be established for unaffected individuals (ofvarying ages, ethnic backgrounds and sexes) without a particularphenotype by determining the biosignature of interest in an unaffectedindividual. For example, a reference value for a reference populationcan be used as a baseline for detection of one or more circulatingbiomarker populations in a test subject. If a sample from a subject hasa level or value that is similar to the reference, the subject can beidentified to not have the disease, or of having a low likelihood ofdeveloping a disease.

Alternatively, reference values or levels can be established forindividuals with a particular phenotype by determining the amount of oneor more populations of vesicles in an individual with the phenotype. Inaddition, an index of values can be generated for a particularphenotype. For example, different disease stages can have differentvalues, such as obtained from individuals with the different diseasestages. A subject's value can be compared to the index and a diagnosisor prognosis of the disease can be determined, such as the disease stageor progression wherein the subject's levels most closely correlate withthe index. In other embodiments, an index of values is generated fortherapeutic efficacies. For example, the level of vesicles ofindividuals with a particular disease can be generated and noted whattreatments were effective for the individual. The levels can be used togenerate values of which is a subject's value is compared, and atreatment or therapy can be selected for the individual, e.g., bypredicting from the levels whether the subject is likely to be aresponder or non-responder for a treatment.

In some embodiments, a reference value is determined for individualsunaffected with a particular cancer, by isolating or detectingcirculating biomarkers with an antigen that specifically targetsbiomarkers for the particular cancer. As a non-limiting example,individuals with varying stages of colorectal cancer and noncancerouspolyps can be surveyed using the same techniques described forunaffected individuals and the levels of circulating vesicles for eachgroup can be determined. In some embodiments, the levels are defined asmeans±standard deviations from at least two separate experiments,performed in at least duplicate or triplicate. Comparisons between thesegroups can be made using statistical tests to determine statisticalsignificance of distinguishing biomarkers observed. In some embodiments,statistical significance is determined using a parametric statisticaltest. The parametric statistical test can comprise, without limitation,a fractional factorial design, analysis of variance (ANOVA), a t-test,least squares, a Pearson correlation, simple linear regression,nonlinear regression, multiple linear regression, or multiple nonlinearregression. Alternatively, the parametric statistical test can comprisea one-way analysis of variance, two-way analysis of variance, orrepeated measures analysis of variance. In other embodiments,statistical significance is determined using a nonparametric statisticaltest. Examples include, but are not limited to, a Wilcoxon signed-ranktest, a Mann-Whitney test, a Kruskal-Wallis test, a Friedman test, aSpearman ranked order correlation coefficient, a Kendall Tau analysis,and a nonparametric regression test. In some embodiments, statisticalsignificance is determined at a p-value of less than 0.05, 0.01, 0.005,0.001, 0.0005, or 0.0001. The p-values can also be corrected formultiple comparisons, e.g., using a Bonferroni correction, amodification thereof, or other technique known to those in the art,e.g., the Hochberg correction, Holm-Bonferroni correction, {umlaut over(S)}idák correction, Dunnett's correction or Tukey's multiplecomparisons. In some embodiments, an ANOVA is followed by Tukey'scorrection for post-test comparing of the biomarkers from eachpopulation.

Reference values can also be established for disease recurrencemonitoring (or exacerbation phase in MS), for therapeutic responsemonitoring, or for predicting responder/non-responder status.

In some embodiments, a reference value for vesicles is determined usingan artificial vesicle, also referred to herein as a synthetic vesicle.Methods for manufacturing artificial vesicles are known to those ofskill in the art, e.g., using liposomes. Artificial vesicles can bemanufactured using methods disclosed in US20060222654 and U.S. Pat. No.4,448,765, which are incorporated herein by reference in its entirety.Artificial vesicles can be constructed with known markers to facilitatecapture and/or detection. In some embodiments, artificial vesicles arespiked into a bodily sample prior to processing. The level of intactsynthetic vesicle can be tracked during processing, e.g., usingfiltration or other isolation methods disclosed herein, to provide acontrol for the amount of vesicles in the initial versus processedsample. Similarly, artificial vesicles can be spiked into a samplebefore or after any processing steps. In some embodiments, artificialvesicles are used to calibrate equipment used for isolation anddetection of vesicles.

Artificial vesicles can be produced and used a control to test theviability of an assay, such as a bead-based assay. The artificialvesicle can bind to both the beads and to the detection antibodies.Thus, the artificial vesicle contains the amino acidsequence/conformation that each of the antibodies binds. The artificialvesicle can comprise a purified protein or a synthetic peptide sequenceto which the antibody binds. The artificial vesicle could be a bead,e.g., a polystyrene bead, that is capable of having biological moleculesattached thereto. If the bead has an available carboxyl group, then theprotein or peptide could be attached to the bead via an available aminegroup, such as using carbodiimide coupling.

In another embodiment, the artificial vesicle can be a polystyrene beadcoated with avidin and a biotin is placed on the protein or peptide ofchoice either at the time of synthesis or via a biotin-maleimidechemistry. The proteins/peptides to be on the bead can be mixed togetherin ratio specific to the application the artificial vesicle is beingused for, and then conjugated to the bead. These artificial vesicles canthen serve as a link between the capture beads and the detectionantibodies, thereby providing a control to show that the components ofthe assay are working properly.

The value can be a quantitative or qualitative value. The value can be adirect measurement of the level of vesicles (example, mass per volume),or an indirect measure, such as the amount of a specific biomarker. Thevalue can be a quantitative, such as a numerical value. In otherembodiments, the value is qualitative, such as no vesicles, low level ofvesicles, medium level, high level of vesicles, or variations thereof.

The reference value can be stored in a database and used as a referencefor the diagnosis, prognosis, theranosis, disease stratification,disease monitoring, treatment monitoring or prediction ofnon-responder/responder status of a disease or condition based on thelevel or amount of circulating biomarkers, such as total amount ofvesicles or microRNA, or the amount of a specific population of vesiclesor microRNA, such as cell-of-origin specific vesicles or microRNA ormicroRNA from vesicles with a specific biosignature. In an illustrativeexample, consider a method of determining a diagnosis for a cancer.Vesicles or other circulating biomarkers from reference subjects withand without the cancer are assessed and stored in the database. Thereference subjects provide biosignature indicative of the cancer or ofanother state, e.g., a healthy state. A sample from a test subject isthen assayed and the microRNA biosignature is compared against those inthe database. If the subject's biosignature correlates more closely withreference values indicative of cancer, a diagnosis of cancer may bemade. Conversely, if the subject's biosignature correlates more closelywith reference values indicative of a healthy state, the subject may bedetermined to not have the disease. One of skill will appreciate thatthis example is non-limiting and can be expanded for assessing otherphenotypes, e.g., other diseases, prognosis, theranosis, diseasestratification, disease monitoring, treatment monitoring or predictionof non-responder/responder status, and the like.

A biosignature for characterizing a phenotype can be determined bydetecting circulating biomarkers such as vesicles, including biomarkersassociate with vesicles such as surface antigens or payload. Thepayload, e.g., protein or species of RNA such as mRNA or microRNA, canbe assessed within a vesicle. Alternately, the payload in a sample isanalyzed to characterize the phenotype without isolating the payloadfrom the vesicles. Many analytical techniques are available to assessvesicles. In some embodiments, vesicle levels are characterized usingmass spectrometry, flow cytometry, immunocytochemical staining, Westernblotting, electrophoresis, chromatography or x-ray crystallography inaccordance with procedures known in the art. For example, vesicles canbe characterized and quantitatively measured using flow cytometry asdescribed in Clayton et al., Journal of Immunological Methods 2001;163-174, which is herein incorporated by reference in its entirety.Vesicle levels may be determined using binding agents as describedabove. For example, a binding agent to vesicles can be labeled and thelabel detected and used to determine the amount of vesicles in a sample.The binding agent can be bound to a substrate, such as arrays orparticles, such as described above. Alternatively, the vesicles may belabeled directly.

Electrophoretic tags or eTags can be used to determine the amount ofvesicles. eTags are small fluorescent molecules linked to nucleic acidsor antibodies and are designed to bind one specific nucleic acidsequence or protein, respectively. After the eTag binds its target, anenzyme is used to cleave the bound eTag from the target. The signalgenerated from the released eTag, called a “reporter,” is proportionalto the amount of target nucleic acid or protein in the sample. The eTagreporters can be identified by capillary electrophoresis. The uniquecharge-to-mass ratio of each eTag reporter—that is, its electricalcharge divided by its molecular weight—makes it show up as a specificpeak on the capillary electrophoresis readout. Thus by targeting aspecific biomarker of a vesicle with an eTag, the amount or level ofvesicles can be determined.

The vesicle level can determined from a heterogeneous population ofvesicles, such as the total population of vesicles in a sample.Alternatively, the vesicles level is determined from a homogenouspopulation, or substantially homogenous population of vesicles, such asthe level of specific cell-of-origin vesicles, such as vesicles fromprostate cancer cells. In yet other embodiments, the level is determinedfor vesicles with a particular biomarker or combination of biomarkers,such as a biomarker specific for prostate cancer. Determining the levelvesicles can be performed in conjunction with determining the biomarkeror combination of biomarkers of a vesicle. Alternatively, determiningthe amount of vesicle may be performed prior to or subsequent todetermining the biomarker or combination of biomarkers of the vesicles.

Determining the amount of vesicles can be assayed in a multiplexedmanner. For example, determining the amount of more than one populationof vesicles, such as different cell-of-origin specific vesicles withdifferent biomarkers or combination of biomarkers, can be performed,such as those disclosed herein.

Performance of a diagnostic or related test is typically assessed usingstatistical measures. The performance of the characterization can beassessed by measuring sensitivity, specificity and related measures. Forexample, a level of circulating biomarkers of interest can be assayed tocharacterize a phenotype, such as detecting a disease. The sensitivityand specificity of the assay to detect the disease is determined.

A true positive is a subject with a characteristic, e.g., a disease ordisorder, correctly identified as having the characteristic. A falsepositive is a subject without the characteristic that the testimproperly identifies as having the characteristic. A true negative is asubject without the characteristic that the test correctly identifies asnot having the characteristic. A false negative is a person with thecharacteristic that the test improperly identifies as not having thecharacteristic. The ability of the test to distinguish between theseclasses provides a measure of test performance.

The specificity of a test is defined as the number of true negativesdivided by the number of actual negatives (i.e., sum of true negativesand false positives). Specificity is a measure of how many subjects arecorrectly identified as negatives. A specificity of 100% means that thetest recognizes all actual negatives—for example, all healthy peoplewill be recognized as healthy. A lower specificity indicates that morenegatives will be determined as positive.

The sensitivity of a test is defined as the number of true positivesdivided by the number of actual positives (i.e., sum of true positivesand false negatives). Sensitivity is a measure of how many subjects arecorrectly identified as positives. A sensitivity of 100% means that thetest recognizes all actual positives—for example, all sick people willbe recognized as sick. A lower sensitivity indicates that more positiveswill be missed by being determined as negative.

The accuracy of a test is defined as the number of true positives andtrue negatives divided by the sum of all true and false positives andall true and false negatives. It provides one number that combinessensitivity and specificity measurements.

Sensitivity, specificity and accuracy are determined at a particulardiscrimination threshold value. For example, a common threshold forprostate cancer (PCa) detection is 4 ng/mL of prostate specific antigen(PSA) in serum. A level of PSA equal to or above the threshold isconsidered positive for PCa and any level below is considered negative.As the threshold is varied, the sensitivity and specificity will alsovary. For example, as the threshold for detecting cancer is increased,the specificity will increase because it is harder to call a subjectpositive, resulting in fewer false positives. At the same time, thesensitivity will decrease. A receiver operating characteristic curve(ROC curve) is a graphical plot of the true positive rate (i.e.,sensitivity) versus the false positive rate (i.e., 1—specificity) for abinary classifier system as its discrimination threshold is varied. TheROC curve shows how sensitivity and specificity change as the thresholdis varied. The Area Under the Curve (AUC) of an ROC curve provides asummary value indicative of a test's performance over the entire rangeof thresholds. The AUC is equal to the probability that a classifierwill rank a randomly chosen positive sample higher than a randomlychosen negative sample. An AUC of 0.5 indicates that the test has a 50%chance of proper ranking, which is equivalent to no discriminatory power(a coin flip also has a 50% chance of proper ranking) An AUC of 1.0means that the test properly ranks (classifies) all subjects. The AUC isequivalent to the Wilcoxon test of ranks.

A biosignature according to the invention can be used to characterize aphenotype with at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, or 70% sensitivity, such as with atleast 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, or87% sensitivity. In some embodiments, the phenotype is characterizedwith at least 87.1, 87.2, 87.3, 87.4, 87.5, 87.6, 87.7, 87.8, 87.9,88.0, or 89% sensitivity, such as at least 90% sensitivity. Thephenotype can be characterized with at least 91, 92, 93, 94, 95, 96, 97,98, 99 or 100% sensitivity.

A biosignature according to the invention can be used to characterize aphenotype of a subject with at least 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, or 97% specificity, such as with at least 97.1, 97.2, 97.3,97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9, 98.0, 98.1, 98.2, 98.3, 98.4,98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6,99.7, 99.8, 99.9 or 100% specificity.

A biosignature according to the invention can be used to characterize aphenotype of a subject, e.g., based on a level of a circulatingbiomarker or other characteristic, with at least 50% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least55% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 60% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 65% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least70% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 75% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 80% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least85% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 86% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 87% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least88% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 89% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 90% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least91% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 92% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 93% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least94% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 95% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 96% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; at least97% sensitivity and at least 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100%specificity; at least 98% sensitivity and at least 60, 65, 70, 75, 80,85, 90, 95, 99, or 100% specificity; at least 99% sensitivity and atleast 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% specificity; orsubstantially 100% sensitivity and at least 60, 65, 70, 75, 80, 85, 90,95, 99, or 100% specificity.

A biosignature according to the invention can be used to characterize aphenotype of a subject with at least 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97% accuracy, such as with atleast 97.1, 97.2, 97.3, 97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9, 98.0,98.1, 98.2, 98.3, 98.4, 98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1, 99.2,99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9 or 100% accuracy.

In some embodiments, a biosignature according to the invention is usedto characterize a phenotype of a subject with an AUC of at least 0.60,0.61, 0.62, 0.63, 0.64, 0.65, 0.66, 0.67, 0.68, 0.69, 0.70, 0.71, 0.72,0.73, 0.74, 0.75, 0.76, 0.77, 0.78, 0.79, 0.80, 0.81, 0.82, 0.83, 0.84,0.85, 0.86, 0.87, 0.88, 0.89, 0.90, 0.91, 0.92, 0.93, 0.94, 0.95, 0.96,or 0.97, such as with at least 0.971, 0.972, 0.973, 0.974, 0.975, 0.976,0.977, 0.978, 0.978, 0.979, 0.980, 0.981, 0.982, 0.983, 0.984, 0.985,0.986, 0.987, 0.988, 0.989, 0.99, 0.991, 0.992, 0.993, 0.994, 0.995,0.996, 0.997, 0.998, 0.999 or 1.00.

Furthermore, the confidence level for determining the specificity,sensitivity, accuracy or AUC, may be determined with at least 50, 51,52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% confidence.

Other related performance measures include positive and negativelikelihood ratios [positive LR=sensitivity/(1-specificity); negativeLR=(1-sensitivity)/specificity]. Such measures can also be used to gaugetest performance according to the methods of the invention.

Classification

Biosignature according to the invention can be used to classify asample. Techniques for discriminate analysis are known to those of skillin the art. For example, a sample can be classified as, or predicted tobe, a responder or non-responder to a given treatment for a givendisease or disorder. Many statistical classification techniques areknown to those of skill in the art. In supervised learning approaches, agroup of samples from two or more groups are analyzed with a statisticalclassification method. Biomarkers can be discovered that can be used tobuild a classifier that differentiates between the two or more groups. Anew sample can then be analyzed so that the classifier can associate thenew with one of the two or more groups. Commonly used supervisedclassifiers include without limitation the neural network (multi-layerperceptron), support vector machines, k-nearest neighbors, Gaussianmixture model, Gaussian, naive Bayes, decision tree and radial basisfunction (RBF) classifiers. Linear classification methods includeFisher's linear discriminant, logistic regression, naive Bayesclassifier, perceptron, and support vector machines (SVMs). Otherclassifiers for use with the invention include quadratic classifiers,k-nearest neighbor, boosting, decision trees, random forests, neuralnetworks, pattern recognition, Bayesian networks and Hidden Markovmodels. One of skill will appreciate that these or other classifiers,including improvements of any of these, are contemplated within thescope of the invention.

Classification using supervised methods is generally performed by thefollowing methodology:

In order to solve a given problem of supervised learning (e.g. learningto recognize handwriting) one has to consider various steps:

1. Gather a training set. These can include, for example, samples thatare from a subject with or without a disease or disorder, subjects thatare known to respond or not respond to a treatment, subjects whosedisease progresses or does not progress, etc. The training samples areused to “train” the classifier.

2. Determine the input “feature” representation of the learned function.The accuracy of the learned function depends on how the input object isrepresented. Typically, the input object is transformed into a featurevector, which contains a number of features that are descriptive of theobject. The number of features should not be too large, because of thecurse of dimensionality; but should be large enough to accuratelypredict the output. The features might include a set of biomarkers suchas those derived from vesicles as described herein.

3. Determine the structure of the learned function and correspondinglearning algorithm. A learning algorithm is chosen, e.g., artificialneural networks, decision trees, Bayes classifiers or support vectormachines. The learning algorithm is used to build the classifier.

4. Build the classifier. The learning algorithm is run the gatheredtraining set. Parameters of the learning algorithm may be adjusted byoptimizing performance on a subset (called a validation set) of thetraining set, or via cross-validation. After parameter adjustment andlearning, the performance of the algorithm may be measured on a test setof naive samples that is separate from the training set.

Once the classifier is determined as described above, it can be used toclassify a sample, e.g., that of a subject who is being analyzed by themethods of the invention. As an example, a classifier can be built usingdata for levels of circulating biomarkers of interest in referencesubjects with and without a disease as the training and test sets.Circulating biomarker levels found in a sample from a test subject areassessed and the classifier is used to classify the subject as with orwithout the disease. As another example, a classifier can be built usingdata for levels of vesicle biomarkers of interest in reference subjectsthat have been found to respond or not respond to certain diseases asthe training and test sets. The vesicle biomarker levels found in asample from a test subject are assessed and the classifier is used toclassify the subject as with or without the disease.

Unsupervised learning approaches can also be used with the invention.Clustering is an unsupervised learning approach wherein a clusteringalgorithm correlates a series of samples without the use the labels. Themost similar samples are sorted into “clusters.” A new sample could besorted into a cluster and thereby classified with other members that itmost closely associates. Many clustering algorithms well known to thoseof skill in the art can be used with the invention, such as hierarchicalclustering.

Biosignatures

A biosignature can be obtained according to the invention by assessing avesicle population, including surface and payload vesicle associatedbiomarkers, and/or circulating biomarkers including microRNA andprotein. A biosignature derived from a subject can be used tocharacterize a phenotype of the subject. A biosignature can furtherinclude the level of one or more additional biomarkers, e.g.,circulating biomarkers or biomarkers associated with a vesicle ofinterest. A biosignature of a vesicle of interest can include particularantigens or biomarkers that are present on the vesicle. The biosignaturecan also include one or more antigens or biomarkers that are carried aspayload within the vesicle, including the microRNA under examination.The biosignature can comprise a combination of one or more antigens orbiomarkers that are present on the vesicle with one or more biomarkersthat are detected in the vesicle. The biosignature can further compriseother information about a vesicle aside from its biomarkers. Suchinformation can include vesicle size, circulating half-life, metabolichalf-life, and specific activity in vivo or in vitro. The biosignaturecan comprise the biomarkers or other characteristics used to build aclassifier.

In some embodiments, the microRNA is detected directly in a biologicalsample. For example, RNA in a bodily fluid can be isolated usingcommercially available kits such as mirVana kits (AppliedBiosystems/Ambion, Austin, Tex.), MagMAX™ RNA Isolation Kit (AppliedBiosystems/Ambion, Austin, Tex.), and QIAzol Lysis Reagent and RNeasyMidi Kit (Qiagen Inc., Valencia Calif.). Particular species of microRNAscan be determined using array or PCR techniques as described below.

In some embodiments, the microRNA payload with vesicles is assessed inorder to characterize a phenotype. The vesicles can be purified orconcentrated prior to determining the biosignature. For example, acell-of-origin specific vesicle can be isolated and its biosignaturedetermined. Alternatively, the biosignature of the vesicle can bedirectly assayed from a sample, without prior purification orconcentration. The biosignature of the invention can be used todetermine a diagnosis, prognosis, or theranosis of a disease orcondition or similar measures described herein. A biosignature can alsobe used to determine treatment efficacy, stage of a disease orcondition, or progression of a disease or condition, orresponder/non-responder status. Furthermore, a biosignature may be usedto determine a physiological state, such as pregnancy.

A characteristic of a vesicle in and of itself can be assessed todetermine a biosignature. The characteristic can be used to diagnose,detect or determine a disease stage or progression, the therapeuticimplications of a disease or condition, or characterize a physiologicalstate. Such characteristics include without limitation the level oramount of vesicles, vesicle size, temporal evaluation of the variationin vesicle half-life, circulating vesicle half-life, metabolic half-lifeof a vesicle, or activity of a vesicle.

Biomarkers that can be included in a biosignature include one or moreproteins or peptides (e.g., providing a protein signature), nucleicacids (e.g. RNA signature as described, or a DNA signature), lipids(e.g. lipid signature), or combinations thereof. In some embodiments,the biosignature can also comprise the type or amount of drug or drugmetabolite present in a vesicle, (e.g., providing a drug signature), assuch drug may be taken by a subject from which the biological sample isobtained, resulting in a vesicle carrying the drug or metabolites of thedrug.

A biosignature can also include an expression level, presence, absence,mutation, variant, copy number variation, truncation, duplication,modification, or molecular association of one or more biomarkers. Agenetic variant, or nucleotide variant, refers to changes or alterationsto a gene or cDNA sequence at a particular locus, including, but notlimited to, nucleotide base deletions, insertions, inversions, andsubstitutions in the coding and non-coding regions. Deletions may be ofa single nucleotide base, a portion or a region of the nucleotidesequence of the gene, or of the entire gene sequence. Insertions may beof one or more nucleotide bases. The genetic variant may occur intranscriptional regulatory regions, untranslated regions of mRNA, exons,introns, or exon/intron junctions. The genetic variant may or may notresult in stop codons, frame shifts, deletions of amino acids, alteredgene transcript splice forms or altered amino acid sequence.

In an embodiment, nucleic acid biomarkers, including nucleic acidpayload within a vesicle, is assessed for nucleotide variants. Thenucleic acid biomarker may comprise one or more RNA species, e.g., mRNA,miRNA, snoRNA, snRNA, rRNAs, tRNAs, siRNA, hnRNA, shRNA, enhancer RNA(eRNA), or a combination thereof. Similarly, DNA payload can be assessedto form a DNA signature.

An RNA signature or DNA signature can also include a mutational,epigenetic modification, or genetic variant analysis of the RNA or DNApresent in the vesicle. Epigenetic modifications include patterns of DNAmethylation. See, e.g., Lesche R. and Eckhardt F., DNA methylationmarkers: a versatile diagnostic tool for routine clinical use. Curr OpinMol Ther. 2007 June; 9(3):222-30, which is incorporated herein byreference in its entirety. Thus, a biomarker can be the methylationstatus of a segment of DNA.

A biosignature can comprise one or more miRNA signatures combined withone or more additional signatures including, but not limited to, an mRNAsignature, DNA signature, protein signature, peptide signature, antigensignature, or any combination thereof. For example, the biosignature cancomprise one or more miRNA biomarkers with one or more DNA biomarkers,one or more mRNA biomarkers, one or more snoRNA biomarkers, one or moreprotein biomarkers, one or more peptide biomarkers, one or more antigenbiomarkers, one or more antigen biomarkers, one or more lipidbiomarkers, or any combination thereof.

A biosignature can comprise a combination of one or more antigens orbinding agents (such as ability to bind one or more binding agents),such as listed in FIGS. 1 and 2, respectively, of International PatentApplication Serial No. PCT/US2011/031479, entitled “CirculatingBiomarkers for Disease” and filed Apr. 6, 2011, which application isincorporated by reference in its entirety herein, or those describedelsewhere herein. The biosignature can further comprise one or moreother biomarkers, such as, but not limited to, miRNA, DNA (e.g. singlestranded DNA, complementary DNA, or noncoding DNA), or mRNA. Thebiosignature of a vesicle can comprise a combination of one or moreantigens, such as shown in FIG. 1 of International Patent ApplicationSerial No. PCT/US2011/031479, one or more binding agents, such as shownin FIG. 2 of International Patent Application Serial No.PCT/US2011/031479, and one or more biomarkers for a condition ordisease, such as listed in FIGS. 3-60 of International PatentApplication Serial No. PCT/US2011/031479. The biosignature can compriseone or more biomarkers, for example miRNA, with one or more antigensspecific for a cancer cell (for example, as shown in FIG. 1 ofInternational Patent Application Serial No. PCT/US2011/031479).

In some embodiments, a vesicle used in the subject methods has abiosignature that is specific to the cell-of-origin and is used toderive disease-specific or biological state specific diagnostic,prognostic or therapy-related biosignatures representative of thecell-of-origin. In other embodiments, a vesicle has a biosignature thatis specific to a given disease or physiological condition that isdifferent from the biosignature of the cell-of-origin for use in thediagnosis, prognosis, staging, therapy-related determinations orphysiological state characterization. Biosignatures can also comprise acombination of cell-of-origin specific and non-specific vesicles.

Biosignatures can be used to evaluate diagnostic criteria such aspresence of disease, disease staging, disease monitoring, diseasestratification, or surveillance for detection, metastasis or recurrenceor progression of disease. A biosignature can also be used clinically inmaking decisions concerning treatment modalities including therapeuticintervention. A biosignature can further be used clinically to maketreatment decisions, including whether to perform surgery or whattreatment standards should be used along with surgery (e.g., eitherpre-surgery or post-surgery). As an illustrative example, a biosignatureof circulating biomarkers that indicates an aggressive form of cancermay call for a more aggressive surgical procedure and/or more aggressivetherapeutic regimen to treat the patient.

A biosignature can be used in therapy related diagnostics to providetests useful to diagnose a disease or choose the correct treatmentregimen, such as provide a theranosis. Theranostics includes diagnostictesting that provides the ability to affect therapy or treatment of adiseased state. Theranostics testing provides a theranosis in a similarmanner that diagnostics or prognostic testing provides a diagnosis orprognosis, respectively. As used herein, theranostics encompasses anydesired form of therapy related testing, including predictive medicine,personalized medicine, integrated medicine, pharmacodiagnostics andDx/Rx partnering. Therapy related tests can be used to predict andassess drug response in individual subjects, i.e., to providepersonalized medicine. Predicting a drug response can be determiningwhether a subject is a likely responder or a likely non-responder to acandidate therapeutic agent, e.g., before the subject has been exposedor otherwise treated with the treatment. Assessing a drug response canbe monitoring a response to a drug, e.g., monitoring the subject'simprovement or lack thereof over a time course after initiating thetreatment. Therapy related tests are useful to select a subject fortreatment who is particularly likely to benefit from the treatment or toprovide an early and objective indication of treatment efficacy in anindividual subject. Thus, a biosignature as disclosed herein mayindicate that treatment should be altered to select a more promisingtreatment, thereby avoiding the great expense of delaying beneficialtreatment and avoiding the financial and morbidity costs ofadministering an ineffective drug(s).

Therapy related diagnostics are also useful in clinical diagnosis andmanagement of a variety of diseases and disorders, which include, butare not limited to cardiovascular disease, cancer, infectious diseases,sepsis, neurological diseases, central nervous system related diseases,endovascular related diseases, and autoimmune related diseases. Therapyrelated diagnostics also aid in the prediction of drug toxicity, drugresistance or drug response. Therapy related tests may be developed inany suitable diagnostic testing format, which include, but are notlimited to, e.g., immunohistochemical tests, clinical chemistry,immunoassay, cell-based technologies, nucleic acid tests or body imagingmethods. Therapy related tests can further include but are not limitedto, testing that aids in the determination of therapy, testing thatmonitors for therapeutic toxicity, or response to therapy testing. Thus,a biosignature can be used to predict or monitor a subject's response toa treatment. A biosignature can be determined at different time pointsfor a subject after initiating, removing, or altering a particulartreatment.

In some embodiments, a determination or prediction as to whether asubject is responding to a treatment is made based on a change in theamount of one or more components of a biosignature (i.e., the microRNA,vesicles and/or biomarkers of interest), an amount of one or morecomponents of a particular biosignature, or the biosignature detectedfor the components. In another embodiment, a subject's condition ismonitored by determining a biosignature at different time points. Theprogression, regression, or recurrence of a condition is determined.Response to therapy can also be measured over a time course. Thus, theinvention provides a method of monitoring a status of a disease or othermedical condition in a subject, comprising isolating or detecting abiosignature from a biological sample from the subject, detecting theoverall amount of the components of a particular biosignature, ordetecting the biosignature of one or more components (such as thepresence, absence, or expression level of a biomarker). Thebiosignatures are used to monitor the status of the disease orcondition.

One or more novel biosignatures of a vesicle can also be identified. Forexample, one or more vesicles can be isolated from a subject thatresponds to a drug treatment or treatment regimen and compared to areference, such as another subject that does not respond to the drugtreatment or treatment regimen. Differences between the biosignaturescan be determined and used to identify other subjects as responders ornon-responders to a particular drug or treatment regimen.

In some embodiments, a biosignature is used to determine whether aparticular disease or condition is resistant to a drug. If a subject isdrug resistant, a physician need not waste valuable time with such drugtreatment. To obtain early validation of a drug choice or treatmentregimen, a biosignature is determined for a sample obtained from asubject. The biosignature is used to assess whether the particularsubject's disease has the biomarker associated with drug resistance.Such a determination enables doctors to devote critical time as well asthe patient's financial resources to effective treatments.

Moreover, biosignature may be used to assess whether a subject isafflicted with disease, is at risk for developing disease or to assessthe stage or progression of the disease. For example, a biosignature canbe used to assess whether a subject has prostate cancer, colon cancer,or other cancer as described herein. Furthermore, a biosignature can beused to determine a stage of a disease or condition, such as coloncancer.

Furthermore, determining the amount of vesicles, such a heterogeneouspopulation of vesicles, and the amount of one or more homogeneouspopulation of vesicles, such as a population of vesicles with the samebiosignature, can be used to characterize a phenotype. For example,determination of the total amount of vesicles in a sample (i.e. notcell-type specific) and determining the presence of one or moredifferent cell-of-origin specific vesicles can be used to characterize aphenotype. Threshold values, or reference values or amounts can bedetermined based on comparisons of normal subjects and subjects with thephenotype of interest, as further described below, and criteria based onthe threshold or reference values determined. The different criteria canbe used to characterize a phenotype.

One criterion can be based on the amount of a heterogeneous populationof vesicles in a sample. In one embodiment, general vesicle markers,such as CD9, CD81, and CD63 can be used to determine the amount ofvesicles in a sample. The expression level of CD9, CD81, CD63, or acombination thereof can be detected and if the level is greater than athreshold level, the criterion is met. In another embodiment, thecriterion is met if level of CD9, CD81, CD63, or a combination thereofis lower than a threshold value or reference value. In anotherembodiment, the criterion can be based on whether the amount of vesiclesis higher than a threshold or reference value. Another criterion can bebased on the amount of vesicles with a specific biosignature. If theamount of vesicles with the specific biosignature is lower than athreshold or reference value, the criterion is met. In anotherembodiment, if the amount of vesicles with the specific biosignature ishigher than a threshold or reference value, the criterion is met. Acriterion can also be based on the amount of vesicles derived from aparticular cell type. If the amount is lower than a threshold orreference value, the criterion is met. In another embodiment, if theamount is higher than a threshold value, the criterion is met.

In a non-limiting example, consider that vesicles from prostate cellsare determined by detecting the biomarker PCSA or PSCA, and that acriterion is met if the level of detected PCSA or PSCA is greater than athreshold level. The threshold can be the level of the same markers in asample from a control cell line or control subject. Another criterioncan be based on whether the amount of vesicles derived from a cancercell or comprising one or more cancer specific biomarkers. For example,the biomarkers B7H3, EpCam, or both, can be determined and a criterionmet if the level of detected B7H3 and/or EpCam is greater than athreshold level or within a pre-determined range. If the amount islower, or higher, than a threshold or reference value, the criterion ismet. A criterion can also be the reliability of the result, such asmeeting a quality control measure or value. A detected amount of B7H3and/or EpCam in a test sample that is above the amount of these markersin a control sample may indicate the presence of a cancer in the testsample.

As described, analysis of multiple markers can be combined to assesswhether a criterion is met. In an illustrative example, a biosignatureis used to assess whether a subject has prostate cancer by detecting oneor more of the general vesicle markers CD9, CD63 and CD81; one or moreprostate epithelial markers including PCSA or PSMA; and one or morecancer markers such as B7H3 and/or EpCam. Higher levels of the markersin a sample from a subject than in a control individual without prostatecancer indicates the presence of the prostate cancer in the subject. Insome embodiments, the multiple markers are assessed in a multiplexfashion.

One of skill will understand that such rules based on meeting criterionas described can be applied to any appropriate biomarker. For example,the criterion can be applied to vesicle characteristics such as amountof vesicles present, amount of vesicles with a particular biosignaturepresent, amount of vesicle payload biomarkers present, amount ofmicroRNA or other circulating biomarkers present, and the like. Theratios of appropriate biomarkers can be determined. As illustrativeexamples, the criterion could be a ratio of an vesicle surface proteinto another vesicle surface protein, a ratio of an vesicle surfaceprotein to a microRNA, a ratio of one vesicle population to anothervesicle population, a ratio of one circulating biomarker to anothercirculating biomarker, etc.

A phenotype for a subject can be characterized based on meeting anynumber of useful criteria. In some embodiments, at least one criterionis used for each biomarker. In some embodiments, at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90 or at least 100criteria are used. For example, for the characterizing of a cancer, anumber of different criteria can be used when the subject is diagnosedwith a cancer: 1) if the amount of microRNA in a sample from a subjectis higher than a reference value; 2) if the amount of a microRNA withincell type specific vesicles (i.e. vesicles derived from a specifictissue or organ) is higher than a reference value; or 3) if the amountof microRNA within vesicles with one or more cancer specific biomarkersis higher than a reference value. Similar rules can apply if the amountof microRNA is less than or the same as the reference. The method canfurther include a quality control measure, such that the results areprovided for the subject if the samples meet the quality controlmeasure. In some embodiments, if the criteria are met but the qualitycontrol is questionable, the subject is reassessed.

In other embodiments, a single measure is determined for assessment ofmultiple biomarkers, and the measure is compared to a reference. Forillustration, a test for prostate cancer might comprise multiplying thelevel of PSA against the level of miR-141 in a blood sample. Thecriterion is met if the product of the levels is above a threshold,indicating the presense of the cancer. As another illustration, a numberof binding agents to general vesicle markers can carry the same label,e.g., the same fluorophore. The level of the detected label can becompared to a threshold.

Criterion can be applied to multiple types of biomarkers in addition tomultiple biomarkers of the same type. For example, the levels of one ormore circulating biomarkers (e.g., RNA, DNA, peptides), vesicles,mutations, etc, can be compared to a reference. Different components ofa biosignature can have different criteria. As a non-limiting example, abiosignature used to diagnose a cancer can include overexpression of onemiR species as compared to a reference and underexpression of a vesiclesurface antigen as compared to another reference.

A biosignature can be determined by comparing the amount of vesicles,the structure of a vesicle, or any other informative characteristic of avesicle. Vesicle structure can be assessed using transmission electronmicroscopy, see for example, Hansen et al., Journal of Biomechanics 31,Supplement 1: 134-134(1) (1998), or scanning electron microscopy.Various combinations of methods and techniques or analyzing one or morevesicles can be used to determine a phenotype for a subject.

A biosignature can include without limitation the presence or absence,copy number, expression level, or activity level of a biomarker. Otheruseful components of a biosignature include the presence of a mutation(e.g., mutations which affect activity of a transcription or translationproduct, such as substitution, deletion, or insertion mutations),variant, or post-translation modification of a biomarker.Post-translational modification of a protein biomarker include withoutlimitation acylation, acetylation, phosphorylation, ubiquitination,deacetylation, alkylation, methylation, amidation, biotinylation,gamma-carboxylation, glutamylation, glycosylation, glycyation,hydroxylation, covalent attachment of heme moiety, iodination,isoprenylation, lipoylation, prenylation, GPI anchor formation,myristoylation, farnesylation, geranylgeranylation, covalent attachmentof nucleotides or derivatives thereof, ADP-ribosylation, flavinattachment, oxidation, palmitoylation, pegylation, covalent attachmentof phosphatidylinositol, phosphopantetheinylation, polysialylation,pyroglutamate formation, racemization of proline by prolyl isomerase,tRNA-mediation addition of amino acids such as arginylation, sulfation,the addition of a sulfate group to a tyrosine, or selenoylation of thebiomarker.

The methods described herein can be used to identify a biosignature thatis associated with a disease, condition or physiological state. Thebiosignature can also be used to determine if a subject is afflictedwith cancer or is at risk for developing cancer. A subject at risk ofdeveloping cancer can include those who may be predisposed or who havepre-symptomatic early stage disease.

A biosignature can also be used to provide a diagnostic or theranosticdetermination for other diseases including but not limited to autoimmunediseases, inflammatory bowel diseases, cardiovascular disease,neurological disorders such as Alzheimer's disease, Parkinson's disease,Multiple Sclerosis, sepsis or pancreatitis or any disease, conditions orsymptoms listed in FIGS. 3-58 of International Patent Application SerialNo. PCT/US2011/031479, entitled “Circulating Biomarkers for Disease” andfiled Apr. 6, 2011, which application is incorporated by reference inits entirety herein.

The biosignature can also be used to identify a given pregnancy statefrom the peripheral blood, umbilical cord blood, or amniotic fluid (e.g.miRNA signature specific to Downs Syndrome) or adverse pregnancy outcomesuch as pre-eclampsia, pre-term birth, premature rupture of membranes,intrauterine growth restriction or recurrent pregnancy loss. Thebiosignature can also be used to indicate the health of the mother, thefetus at all developmental stages, the pre-implantation embryo or anewborn.

A biosignature can be used for pre-symptomatic diagnosis. Furthermore,the biosignature can be used to detect disease, determine disease stageor progression, determine the recurrence of disease, identify treatmentprotocols, determine efficacy of treatment protocols or evaluate thephysiological status of individuals related to age and environmentalexposure.

Monitoring a biosignature of a vesicle can also be used to identifytoxic exposures in a subject including, but not limited to, situationsof early exposure or exposure to an unknown or unidentified toxic agent.Without being bound by any one specific theory for mechanism of action,vesicles can shed from damaged cells and in the process compartmentalizespecific contents of the cell including both membrane components andengulfed cytoplasmic contents. Cells exposed to toxic agents/chemicalsmay increase vesicle shedding to expel toxic agents or metabolitesthereof, thus resulting in increased vesicle levels. Thus, monitoringvesicle levels, vesicle biosignature, or both, allows assessment of anindividual's response to potential toxic agent(s).

A vesicle and/or other biomarkers of the invention can be used toidentify states of drug-induced toxicity or the organ injured, bydetecting one or more specific antigen, binding agent, biomarker, or anycombination thereof. The level of vesicles, changes in the biosignatureof a vesicle, or both, can be used to monitor an individual for acute,chronic, or occupational exposures to any number of toxic agentsincluding, but not limited to, drugs, antibiotics, industrial chemicals,toxic antibiotic metabolites, herbs, household chemicals, and chemicalsproduced by other organisms, either naturally occurring or synthetic innature. In addition, a biosignature can be used to identify conditionsor diseases, including cancers of unknown origin, also known as cancersof unknown primary (CUP).

A vesicle may be isolated from a biological sample as previouslydescribed to arrive at a heterogeneous population of vesicles. Theheterogeneous population of vesicles can then be contacted withsubstrates coated with specific binding agents designed to rule out oridentify antigen specific characteristics of the vesicle population thatare specific to a given cell-of-origin. Further, as described above, thebiosignature of a vesicle can correlate with the cancerous state ofcells. Compounds that inhibit cancer in a subject may cause a change,e.g., a change in biosignature of a vesicle, which can be monitored byserial isolation of vesicles over time and treatment course. The levelof vesicles or changes in the level of vesicles with a specificbiosignature can be monitored.

In an aspect, characterizing a phenotype of a subject comprises a methodof determining whether the subject is likely to respond or not respondto a therapy. The methods of the invention also include determining newbiosignatures useful in predicting whether the subject is likely torespond or not. One or more subjects that respond to a therapy(responders) and one or more subjects that do not respond to the sametherapy (non-responders) can have their vesicles interrogated.Interrogation can be performed to identify vesicle biosignatures thatclassify a subject as a responder or non-responder to the treatment ofinterest. In some aspects, the presence, quantity, and payload of avesicle are assayed. The payload of a vesicle includes, for example,internal proteins, nucleic acids such as miRNA, lipids or carbohydrates.

The presence or absence of a biosignature in responders but not in thenon-responders can be used for theranosis. A sample from responders maybe analyzed for one or more of the following: amount of vesicles, amountof a unique subset or species of vesicles, biomarkers in such vesicles,biosignature of such vesicles, etc. In one instance, vesicles such asmicrovesicles or exosomes from responders and non-responders areanalyzed for the presence and/or quantity of one or more miRNAs, such asmiRNA 122, miR-548c-5p, miR-362-3p, miR-422a, miR-597, miR-429,miR-200a, and/or miR-200b. A difference in biosignatures betweenresponders and non-responders can be used for theranosis. In anotherembodiment, vesicles are obtained from subjects having a disease orcondition. Vesicles are also obtained from subjects free of such diseaseor condition. The vesicles from both groups of subjects are assayed forunique biosignatures that are associated with all subjects in that groupbut not in subjects from the other group. Such biosignatures orbiomarkers can then used as a diagnostic for the presence or absence ofthe condition or disease, or to classify the subject as belonging on oneof the groups (those with/without disease, aggressive/non-aggressivedisease, responder/non-responder, etc).

In an aspect, characterizing a phenotype of a subject comprises a methodof staging a disease. The methods of the invention also includedetermining new biosignatures useful in staging. In an illustrativeexample, vesicles are assayed from patients having a stage I cancer andpatients having stage 11 or stage III of the same cancer. In someembodiments, vesicles are assayed in patients with metastatic disease. Adifference in biosignatures or biomarkers between vesicles from eachgroup of patient is identified (e.g., vesicles from stage III cancer mayhave an increased expression of one or more genes or miRNA's), therebyidentifying a biosignature or biomarker that distinguishes differentstages of a disease. Such biosignature can then be used to stagepatients having the disease.

In some instances, a biosignature is determined by assaying vesiclesfrom a subject over a period of time, e.g., daily, semiweekly, weekly,biweekly, semimonthly, monthly, bimonthly, semiquarterly, quarterly,semiyearly, biyearly or yearly. For example, the biosignatures inpatients on a given therapy can be monitored over time to detectsignatures indicative of responders or non-responders for the therapy.Similarly, patients with differing stages of disease have their vesiclesinterrogated over time. The payload or physical attributes of thevesicles in each point in time can be compared. A temporal pattern canthus form a biosignature that can then be used for theranosis,diagnosis, prognosis, disease stratification, treatment monitoring,disease monitoring or making a prediction of responder/non-responderstatus. As an illustrative example only, an increasing amount of abiomarker (e.g., miR 122) in vesicles over a time course is associatedwith metastatic cancer, as opposed to a stagnant amounts of thebiomarker in vesicles over the time course that are associated withnon-metastatic cancer. A time course may last over at least 1 week, 2weeks, 3 weeks, 4 weeks, 1 month, 6 weeks, 8 weeks, 2 months, 10 weeks,12 weeks, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9months, 10 months, 11 months, 12 months, one year, 18 months, 2 years,or at least 3 years.

The level of vesicles, level of vesicles with a specific biosignature,or a biosignature of a vesicle can also be used to assess the efficacyof a therapy for a condition. For example, the level of vesicles, levelof vesicles with a specific biosignature, or a biosignature of a vesiclecan be used to assess the efficacy of a cancer treatment, e.g.,chemotherapy, radiation therapy, surgery, or any other therapeuticapproach useful for inhibiting cancer in a subject. In addition, abiosignature can be used in a screening assay to identify candidate ortest compounds or agents (e.g., proteins, peptides, peptidomimetics,peptoids, small molecules or other drugs) that have a modulatory effecton the biosignature of a vesicle. Compounds identified via suchscreening assays may be useful, for example, for modulating, e.g.,inhibiting, ameliorating, treating, or preventing conditions ordiseases.

For example, a biosignature for a vesicle can be obtained from a patientwho is undergoing successful treatment for a particular cancer. Cellsfrom a cancer patient not being treated with the same drug can becultured and vesicles from the cultures obtained for determiningbiosignatures. The cells can be treated with test compounds and thebiosignature of the vesicles from the cultures can be compared to thebiosignature of the vesicles obtained from the patient undergoingsuccessful treatment. The test compounds that results in biosignaturesthat are similar to those of the patient undergoing successful treatmentcan be selected for further studies.

The biosignature of a vesicle can also be used to monitor the influenceof an agent (e.g., drug compounds) on the biosignature in clinicaltrials. Monitoring the level of vesicles, changes in the biosignature ofa vesicle, or both, can also be used in a method of assessing theefficacy of a test compound, such as a test compound for inhibitingcancer cells.

In addition to diagnosing or confirming the presence of or risk fordeveloping a disease, condition or a syndrome, the methods andcompositions disclosed herein also provide a system for optimizing thetreatment of a subject having such a disease, condition or syndrome. Thelevel of vesicles, the biosignature of a vesicle, or both, can also beused to determine the effectiveness of a particular therapeuticintervention (pharmaceutical or non-pharmaceutical) and to alter theintervention to 1) reduce the risk of developing adverse outcomes, 2)enhance the effectiveness of the intervention or 3) identify resistantstates. Thus, in addition to diagnosing or confirming the presence of orrisk for developing a disease, condition or a syndrome, the methods andcompositions disclosed herein also provide a system for optimizing thetreatment of a subject having such a disease, condition or syndrome. Forexample, a therapy-related approach to treating a disease, condition orsyndrome by integrating diagnostics and therapeutics to improve thereal-time treatment of a subject can be determined by identifying thebiosignature of a vesicle.

Tests that identify the level of vesicles, the biosignature of avesicle, or both, can be used to identify which patients are most suitedto a particular therapy, and provide feedback on how well a drug isworking, so as to optimize treatment regimens. For example, inpregnancy-induced hypertension and associated conditions,therapy-related diagnostics can flexibly monitor changes in importantparameters (e.g., cytokine and/or growth factor levels) over time, tooptimize treatment.

Within the clinical trial setting of investigational agents as definedby the FDA, MDA, EMA, USDA, and EMEA, therapy-related diagnostics asdetermined by a biosignature disclosed herein, can provide keyinformation to optimize trial design, monitor efficacy, and enhance drugsafety. For instance, for trial design, therapy-related diagnostics canbe used for patient stratification, determination of patient eligibility(inclusion/exclusion), creation of homogeneous treatment groups, andselection of patient samples that are optimized to a matched casecontrol cohort. Such therapy-related diagnostic can therefore providethe means for patient efficacy enrichment, thereby minimizing the numberof individuals needed for trial recruitment. For example, for efficacy,therapy-related diagnostics are useful for monitoring therapy andassessing efficacy criteria. Alternatively, for safety, therapy-relateddiagnostics can be used to prevent adverse drug reactions or avoidmedication error and monitor compliance with the therapeutic regimen.

In some embodiments, the invention provides a method of identifyingresponder and non-responders to a treatment undergoing clinical trials,comprising detecting biosignatures comprising circulating biomarkers insubjects enrolled in the clinical trial, and identifying biosignaturesthat distinguish between responders and non-responders. In a furtherembodiment, the biosignatures are measured in a drug naive subject andused to predict whether the subject will be a responder ornon-responder. The prediction can be based upon whether thebiosignatures of the drug naive subject correlate more closely with theclinical trial subjects identified as responders, thereby predictingthat the drug naive subject will be a responder. Conversely, if thebiosignatures of the drug naive subject correlate more closely with theclinical trial subjects identified as non-responders, the methods of theinvention can predict that the drug naive subject will be anon-responder. The prediction can therefore be used to stratifypotential responders and non-responders to the treatment. In someembodiments, the prediction is used to guide a course of treatment,e.g., by helping treating physicians decide whether to administer thedrug. In some embodiments, the prediction is used to guide selection ofpatients for enrollment in further clinical trials. In a non-limitingexample, biosignatures that predict responder/non-responder status inPhase II trials can be used to select patients for a Phase III trial,thereby increasing the likelihood of response in the Phase III patientpopulation. One of skill will appreciate that the method can be adaptedto identify biosignatures to stratify subjects on criteria other thanresponder/non-responder status. In one embodiment, the criterion istreatment safety. Therefore the method is followed as above to identifysubjects who are likely or not to have adverse events to the treatment.In a non-limiting example, biosignatures that predict safety profile inPhase II trials can be used to select patients for a Phase III trial,thereby increasing the treatment safety profile in the Phase III patientpopulation.

Therefore, the level of vesicles, the biosignature of a vesicle, orboth, can be used to monitor drug efficacy, determine response orresistance to a given drug, or both, thereby enhancing drug safety. Forexample, in colon cancer, vesicles are typically shed from colon cancercells and can be isolated from the peripheral blood and used to isolateone or more biomarkers e.g., KRAS mRNA which can then be sequenced todetect KRAS mutations. In the case of mRNA biomarkers, the mRNA can bereverse transcribed into cDNA and sequenced (e.g., by Sanger sequencing,pyrosequencing, NextGen sequencing, RT-PCR assays) to determine if thereare mutations present that confer resistance to a drug (e.g., cetuximabor panitumimab). In another example, vesicles that are specifically shedfrom lung cancer cells are isolated from a biological sample and used toisolate a lung cancer biomarker, e.g., EGFR mRNA. The EGFR mRNA isprocessed to cDNA and sequenced to determine if there are EGFR mutationspresent that show resistance or response to specific drugs or treatmentsfor lung cancer.

One or more biosignatures can be grouped so that information obtainedabout the set of biosignatures in a particular group provides areasonable basis for making a clinically relevant decision, such as butnot limited to a diagnosis, prognosis, or management of treatment, suchas treatment selection.

As with most diagnostic markers, it is often desirable to use the fewestnumber of markers sufficient to make a correct medical judgment. Thisprevents a delay in treatment pending further analysis as wellinappropriate use of time and resources.

Also disclosed herein are methods of conducting retrospective analysison samples (e.g., serum and tissue biobanks) for the purpose ofcorrelating qualitative and quantitative properties, such asbiosignatures of vesicles, with clinical outcomes in terms of diseasestate, disease stage, progression, prognosis; therapeutic efficacy orselection; or physiological conditions. Furthermore, methods andcompositions disclosed herein are used for conducting prospectiveanalysis on a sample (e.g., serum and/or tissue collected fromindividuals in a clinical trial) for the purpose of correlatingqualitative and quantitative biosignatures of vesicles with clinicaloutcomes in terms of disease state, disease stage, progression,prognosis; therapeutic efficacy or selection; or physiologicalconditions can also be performed. As used herein, a biosignature for avesicle can be used to identify a cell-of-origin specific vesicle.Furthermore, a biosignature can be determined based on a surface markerprofile of a vesicle or contents of a vesicle.

The biosignatures used to characterize a phenotype according to theinvention can comprise multiple components (e.g., microRNA, vesicles orother biomarkers) or characteristics (e.g., vesicle size or morphology).The biosignatures can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, or 100components or characteristics. A biosignature with more than onecomponent or characteristic, such as at least 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, or 100components, may provide higher sensitivity and/or specificity incharacterizing a phenotype. In some embodiments, assessing a pluralityof components or characteristics provides increased sensitivity and/orspecificity as compared to assessing fewer components orcharacteristics. On the other hand, it is often desirable to use thefewest number of components or characteristics sufficient to make acorrect medical judgment. Fewer markers can avoid statisticaloverfitting of a classifier and can prevent a delay in treatment pendingfurther analysis as well inappropriate use of time and resources. Thus,the methods of the invention comprise determining an optimal number ofcomponents or characteristics.

A biosignature according to the invention can be used to characterize aphenotype with a sensitivity, specificity, accuracy, or similarperformance metric as described above. The biosignatures can also beused to build a classifier to classify a sample as belonging to a group,such as belonging to a group having a disease or not, a group having anaggressive disease or not, or a group of responders or non-responders.In one embodiment, a classifier is used to determine whether a subjecthas an aggressive or non-aggressive cancer. In the illustrative case ofprostate cancer, this can help a physician to determine whether to watchthe cancer, i.e., prescribe “watchful waiting,” or perform aprostatectomy. In another embodiment, a classifier is used to determinewhether a breast cancer patient is likely to respond or not totamoxifen, thereby helping the physician to determine whether or not totreat the patient with tamoxifen or another drug.

Biomarkers

A biosignature used to characterize a phenotype can comprise one or morebiomarkers. The biomarker can be a circulating marker, a membraneassociated marker, or a component present within a vesicle or on avesicle's surface. These biomarkers include without limitation a nucleicacid (e.g. RNA (mRNA, miRNA, etc.) or DNA), protein, peptide,polypeptide, antigen, lipid, carbohydrate, or proteoglycan.

The biosignature can include the presence or absence, expression level,mutational state, genetic variant state, or any modification (such asepigenetic modification, or post-translation modification) of abiomarker (e.g. any one or more biomarker listed in FIGS. 1, 3-60 ofInternational Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein). Theexpression level of a biomarker can be compared to a control orreference, to determine the overexpression or underexpression (orupregulation or downregulation) of a biomarker in a sample. In someembodiments, the control or reference level comprises the amount of asame biomarker, such as a miRNA, in a control sample from a subject thatdoes not have or exhibit the condition or disease. In anotherembodiment, the control of reference levels comprises that of ahousekeeping marker whose level is minimally affected, if at all, indifferent biological settings such as diseased versus non-diseasedstates. In yet another embodiment, the control or reference levelcomprises that of the level of the same marker in the same subject butin a sample taken at a different time point. Other types of controls aredescribed herein.

Nucleic acid biomarkers include various RNA or DNA species. For example,the biomarker can be mRNA, microRNA (miRNA), small nucleolar RNAs(snoRNA), small nuclear RNAs (snRNA), ribosomal RNAs (rRNA),heterogeneous nuclear RNA (hnRNA), ribosomal RNAS (rRNA), siRNA,transfer RNAs (tRNA), or shRNA. The DNA can be double-stranded DNA,single stranded DNA, complementary DNA, or noncoding DNA. miRNAs areshort ribonucleic acid (RNA) molecules which average about 22nucleotides long. miRNAs act as post-transcriptional regulators thatbind to complementary sequences in the three prime untranslated regions(3′ UTRs) of target messenger RNA transcripts (mRNAs), which can resultin gene silencing. One miRNA may act upon 1000s of mRNAs. miRNAs playmultiple roles in negative regulation, e.g., transcript degradation andsequestering, translational suppression, and may also have a role inpositive regulation, e.g., transcriptional and translational activation.By affecting gene regulation, miRNAs can influence many biologicprocesses. Different sets of expressed miRNAs are found in differentcell types and tissues.

Biomarkers for use with the invention further include peptides,polypeptides, or proteins, which terms are used interchangeablythroughout unless otherwise noted. In some embodiments, the proteinbiomarker comprises its modification state, truncations, mutations,expression level (such as overexpression or underexpression as comparedto a reference level), and/or post-translational modifications, such asdescribed above. In a non-limiting example, a biosignature for a diseasecan include a protein having a certain post-translational modificationthat is more prevalent in a sample associated with the disease thanwithout.

A biosignature may include a number of the same type of biomarkers(e.g., two or more different microRNA or mRNA species) or one or more ofdifferent types of biomarkers (e.g. mRNAs, miRNAs, proteins, peptides,ligands, and antigens).

One or more biosignatures can comprise at least one biomarker selectedfrom those listed in FIGS. 1, 3-60 of International Patent ApplicationSerial No. PCT/US2011/031479, entitled “Circulating Biomarkers forDisease” and filed Apr. 6, 2011, which application is incorporated byreference in its entirety herein. A specific cell-of-origin biosignaturemay include one or more biomarkers. FIGS. 3-58 of International PatentApplication Serial No. PCT/US2011/031479 depict tables which lists anumber of disease or condition specific biomarkers that can be derivedand analyzed from a vesicle. The biomarker can also be CD24, midkine,hepcidin, TMPRSS2-ERG, PCA-3, PSA, EGFR, EGFRvIII, BRAF variant, MET,cKit, PDGFR, Wnt, beta-catenin, K-ras, H-ras, N-ras, Raf, N-myc, c-myc,IGFR, PI3K, Akt, BRCA1, BRCA2, PTEN, VEGFR-2, VEGFR-1, Tie-2, TEM-1,CD276, HER-2, HER-3, or HER-4. The biomarker can also be annexin V,CD63, Rab-5b, or caveolin, or a miRNA, such as let-7a; miR-15b; miR-16;miR-19b; miR-21; miR-26a; miR-27a; miR-92; miR-93; miR-320 or miR-20.The biomarker can also be of any gene or fragment thereof as disclosedin PCT Publication No. WO2009/100029, such as those listed in Tables3-15 therein.

In another embodiment, a vesicle comprises a cell fragment or cellulardebris derived from a rare cell, such as described in PCT PublicationNo. WO2006054991. One or more biomarkers, such as CD 146, CD 105, CD31,CD 133, CD 106, or a combination thereof, can be assessed for thevesicle. In one embodiment, a capture agent for the one or morebiomarkers is used to isolate or detect a vesicle. In some embodiments,one or more of the biomarkers CD45, cytokeratin (CK) 8, CK18, CK19,CK20, CEA, EGFR, GUC, EpCAM, VEGF, TS, Muc-1, or a combination thereofis assessed for a vesicle. In one embodiment, a tumor-derived vesicle isCD45−, CK+ and comprises a nucleic acid, wherein the membrane vesiclehas an absence of, or low expression or detection of CD45, hasdetectable expression of a cytokeratin (such as CK8, CK18, CK19, orCK20), and detectable expression of a nucleic acid.

Any number of useful biomarkers that can be assessed as part of avesicle biosignature are disclosed throughout the application, includingwithout limitation CD9, EphA2, EGFR, B7H3, PSM, PCSA, CD63, STEAP, CD81,ICAM1, A33, DR3, CD66e, MFG-E8, TROP-2, Mammaglobin, Hepsin, NPGP/NPFF2,PSCA, 5T4, NGAL, EpCam, neurokinin receptor-1 (NK-1 or NK-1R), NK-2,Pai-1, CD45, CD10, HER2/ERBB2, AGTR1, NPY1R, MUC1, ESA, CD133, GPR30,BCA225, CD24, CA15.3 (MUC1 secreted), CA27.29 (MUC1 secreted), NMDAR1,NMDAR2, MAGEA, CTAG1B, NY-ESO-1, SPB, SPC, NSE, PGP9.5, P2RX7, NDUFB7,NSE, GAL3, osteopontin, CHI3L1, IC3b, mesothelin, SPA, AQPS, GPCR,hCEA-CAM, PTP IA-2, CABYR, TMEM211, ADAM28, UNC93A, MUC17, MUC2,IL10R-beta, BCMA, HVEM/TNFRSF14, Trappin-2 Elafin, ST2/IL1 R4, TNFRF14,CEACAM1, TPA1, LAMP, WF, WH1000, PECAM, BSA, TNFR, or a combinationthereof.

Other biomarkers useful for assessment in methods and compositionsdisclosed herein include those associated with conditions orphysiological states as disclosed in U.S. Pat. Nos. 6,329,179 and7,625,573; U.S. Patent Publication Nos. 2002/106684, 2004/005596,2005/0159378, 2005/0064470, 2006/116321, 2007/0161004, 2007/0077553,2007/104738, 2007/0298118, 2007/0172900, 2008/0268429, 2010/0062450,2007/0298118, 2009/0220944 and 2010/0196426; U.S. patent applicationSer. Nos. 12/524,432, 12/524,398, 12/524,462; Canadian Patent CA2453198; and International PCT Patent Publication Nos. WO1994022018,WO2001036601, WO2003063690, WO2003044166, WO2003076603, WO2005121369,WO2005118806, WO/2005/078124, WO2007126386, WO2007088537, WO2007103572,WO2009019215, WO2009021322, WO2009036236, WO2009100029, WO2009015357,WO2009155505, WO 2010/065968 and WO 2010/070276; each of which patent orapplication is incorporated herein by reference in their entirety. Thebiomarkers disclosed in these patents and applications, includingvesicle biomarkers and microRNAs, can be assessed as part of a signaturefor characterizing a phenotype, such as providing a diagnosis, prognosisor theranosis of a cancer or other disease. Furthermore, the methods andtechniques disclosed therein can be used to assess biomarkers, includingvesicle biomarkers and microRNAs.

Another group of useful biomarkers for assessment in methods andcompositions disclosed herein include those associated with cancerdiagnostics, prognostics and theranostics as disclosed in U.S. Pat. Nos.6,692,916, 6,960,439, 6,964,850, 7,074,586; U.S. patent application Ser.Nos. 11/159,376, 11/804,175, 12/594,128, 12/514,686, 12/514,775,12/594,675, 12/594,911, 12/594,679, 12/741,787, 12/312,390; andInternational PCT Patent Application Nos. PCT/US2009/049935,PCT/US2009/063138, PCT/US2010/000037; each of which patent orapplication is incorporated herein by reference in their entirety.Useful biomarkers further include those described in U.S. patentapplication Ser. No. 10/703,143 and U.S. Ser. No. 10/701,391 forinflammatory disease; Ser. No. 11/529,010 for rheumatoid arthritis; Ser.Nos. 11/454,553 and 11/827,892 for multiple sclerosis; Ser. No.11/897,160 for transplant rejection; Ser. No. 12/524,677 for lupus;PCT/US2009/048684 for osteoarthritis; Ser. No. 10/742,458 for infectiousdisease and sepsis; Ser. No. 12/520,675 for sepsis; each of which patentor application is incorporated herein by reference in their entirety.The biomarkers disclosed in these patents and applications, includingmRNAs, can be assessed as part of a signature for characterizing aphenotype, such as providing a diagnosis, prognosis or theranosis of acancer or other disease. Furthermore, the methods and techniquesdisclosed therein can be used to assess biomarkers, including vesiclebiomarkers and microRNAs.

Still other biomarkers useful for assessment in methods and compositionsdisclosed herein include those associated with conditions orphysiological states as disclosed in Wieczorek et al., Isolation andcharacterization of an RNA-proteolipid complex associated with themalignant state in humans, Proc Natl Acad Sci USA. 1985 May;82(10):3455-9; Wieczorek et al., Diagnostic and prognostic value ofRNA-proteolipid in sera of patients with malignant disorders followingtherapy: first clinical evaluation of a novel tumor marker, Cancer Res.1987 Dec. 1; 47(23):6407-12; Escola et al. Selective enrichment oftetraspan proteins on the internal vesicles of multivesicular endosomesand on exosomes secreted by human B-lymphocytes. J. Biol. Chem. (1998)273:20121-27; Pileri et al. Binding of hepatitis C virus to CD81Science, (1998) 282:938-41); Kopreski et al. Detection of TumorMessenger RNA in the Serum of Patients with Malignant Melanoma, Clin.Cancer Res. (1999) 5:1961-1965; Carr et al. Circulating MembraneVesicles in Leukemic Blood, Cancer Research, (1985) 45:5944-51; Weichertet al. Cytoplasmic CD24 expression in colorectal cancer independentlycorrelates with shortened patient survival. Clinical Cancer Research,2005, 11:6574-81); Iorio et al. MicroRNA gene expression deregulation inhuman breast cancer. Cancer Res (2005) 65:7065-70; Taylor et al.Tumour-derived exosomes and their role in cancer-associated T-cellsignaling defects British J Cancer (2005) 92:305-11; Valadi et al.Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism ofgenetic exchange between cells Nature Cell Biol (2007) 9:654-59; Tayloret al. Pregnancy-associated exosomes and their modulation of T cellsignaling J Immunol (2006) 176:1534-42; Koga et al. Purification,characterization and biological significance of tumor-derived exosomesAnticancer Res (2005) 25:3703-08; Seligson et al. Epithelial celladhesion molecule (KSA) expression: pathobiology and its role as anindependent predictor of survival in renal cell carcinoma Clin CancerRes (2004) 10:2659-69; Clayton et al. (Antigen-presenting cell exosomesare protected from complement-mediated lysis by expression of CD55 andCD59. Eur J Immunol (2003) 33:522-31); Simak et al. Cell MembraneMicroparticles in Blood and Blood Products: Potentially PathogenicAgents and Diagnostic Markers Trans Med Reviews (2006) 20:1-26; Choi etal. Proteomic analysis of microvesicles derived from human colorectalcancer cells J Proteome Res (2007) 6:4646-4655; Iero et al.Tumour-released exosomes and their implications in cancer immunity CellDeath Diff (2008) 15:80-88; Baj-Krzyworzeka et al. Tumour-derivedmicrovesicles carry several surface determinants and mRNA of tumourcells and transfer some of these determinants to monocytes CencerImmunol Immunother (2006) 55:808-18; Admyre et al. B cell-derivedexosomes can present allergen peptides and activate allergen-specific Tcells to proliferate and produce TH2-like cytokines J Allergy ClinImmunol (2007) 120:1418-1424; Aoki et al. Identification andcharacterization of microvesicles secreted by 3T3-L1 adipocytes:redox-and hormone dependent induction of milk fat globule-epidermalgrowth factor 8-associated microvesicles Endocrinol (2007)148:3850-3862; Baj-Krzyworzeka et al. Tumour-derived microvesicles carryseveral surface determinants and mRNA of tumour cells and transfer someof these determinants to monocytes Cencer Immunol Immunother (2006)55:808-18; Skog et al. Glioblastoma microvesicles transport RNA andproteins that promote tumour growth and provide diagnostic biomarkersNature Cell Biol (2008) 10:1470-76; El-Hefnawy et al. Characterizationof amplifiable, circulating RNA in plasma and its potential as a toolfor cancer diagnostics Clin Chem (2004) 50:564-573; Pisitkun et al.,Proc Natl Acad Sci USA, 2004; 101:13368-13373; Mitchell et al., Canurinary exosomes act as treatment response markers in Prostate Cancer?,Journal of Translational Medicine 2009, 7:4; Clayton et al., HumanTumor-Derived Exosomes Selectively Impair Lymphocyte Responses toInterleukin-2, Cancer Res 2007; 67: (15). Aug. 1, 2007; Rabesandratanaet al. Decay-accelerating factor (CD55) and membrane inhibitor ofreactive lysis (CD59) are released within exosomes during In vitromaturation of reticulocytes. Blood 91:2573-2580 (1998); Lamparski et al.Production and characterization of clinical grade exosomes derived fromdendritic cells. J Immunol Methods 270:211-226 (2002); Keller et al.CD24 is a marker of exosomes secreted into urine and amniotic fluid.Kidney Int'l 72:1095-1102 (2007); Runz et al. Malignant ascites-derivedexosomes of ovarian carcinoma patients contain CD24 and EpCAM. Gyn Oncol107:563-571 (2007); Redman et al. Circulating microparticles in normalpregnancy and preeclampsia placenta. 29:73-77 (2008); Gutwein et al.Cleavage of L 1 in exosomes and apoptotic membrane vesicles releasedfrom ovarian carcinoma cells. Clin Cancer Res 11:2492-2501 (2005);Kristiansen et al., CD24 is an independent prognostic marker of survivalin nonsmall cell lung cancer patients, Brit J Cancer 88:231-236 (2003);Lim and Oh, The Role of CD24 in Various Human Epithelial Neoplasias,Pathol Res Pract 201:479-86 (2005); Matutes et al., The Immunophenotypeof Splenic Lymphoma with Villous Lymphocytes and its Relevance to theDifferential Diagnosis With Other B-Cell Disorders, Blood 83:1558-1562(1994); Pirruccello and Lang, Differential Expression of CD24-RelatedEpitopes in Mycosis Fungoides/Sezary Syndrome: A Potential Marker forCirculating Sezary Cells, Blood 76:2343-2347 (1990). The biomarkersdisclosed in these publications, including vesicle biomarkers andmicroRNAs, can be assessed as part of a signature for characterizing aphenotype, such as providing a diagnosis, prognosis or theranosis of acancer or other disease. Furthermore, the methods and techniquesdisclosed therein can be used to assess biomarkers, including vesiclebiomarkers and microRNAs.

Still other biomarkers useful for assessment in methods and compositionsdisclosed herein include those associated with conditions orphysiological states as disclosed in Rajendran et al., Proc Natl AcadSci USA 2006; 103:11172-11177, Taylor et al., Gynecol Oncol 2008;110:13-21, Zhou et al., Kidney Int 2008; 74:613-621, Buning et al.,Immunology 2008, Prado et al. J Immunol 2008; 181:1519-1525, Vella etal. (2008) Vet Immunol Immunopathol 124(3-4): 385-93, Gould et al.(2003). Proc Natl Acad Sci USA 100(19): 10592-7, Fang et al. (2007).PLoS Biol 5(6): e158, Chen, B. J. and R. A. Lamb (2008). Virology372(2): 221-32, Bhatnagar, S, and J. S. Schorey (2007). J Biol Chem282(35): 25779-89, Bhatnagar et al. (2007) Blood 110(9): 3234-44,Yuyama, et al. (2008). J Neurochem 105(1): 217-24, Gomes et al. (2007).Neurosci Lett 428(1): 43-6, Nagahama et al. (2003). Autoimmunity 36(3):125-31, Taylor, D. D., S. Akyol, et al. (2006). J Immunol 176(3):1534-42, Peche, et al. (2006). Am J Transplant 6(7): 1541-50, Zero, M.,M. Valenti, et al. (2008). Cell Death and Differentiation 15: 80-88,Gesierich, S., I. Berezoversuskiy, et al. (2006), Cancer Res 66(14):7083-94, Clayton, A., A. Turkes, et al. (2004). Faseb J 18(9): 977-9,Skriner., K Adolph, et al. (2006). Arthritis Rheum 54(12): 3809-14,Brouwer, R., G. J. Pruijn, et al. (2001). Arthritis Res 3(2): 102-6,Kim, S. H., N Bianco, et al. (2006). Mol Ther 13(2): 289-300, Evans, C.H., S. C. Ghivizzani, et al. (2000). Clin Orthop Relat Res (379 Suppl):S300-7, Zhang, H. G., C. Liu, et al. (2006). J Immunol 176(12): 7385-93,Van Niel, G., J. Mallegol, et al. (2004). Gut 52: 1690-1697, Fiasse, R.and O. Dewit (2007). Expert Opinion on Therapeutic Patents 17(12):1423-1441(19). The biomarkers disclosed in these publications, includingvesicle biomarkers and microRNAs, can be assessed as part of a signaturefor characterizing a phenotype, such as providing a diagnosis, prognosisor theranosis of a cancer or other disease. Furthermore, the methods andtechniques disclosed therein can be used to assess biomarkers, includingvesicle biomarkers and microRNAs.

In another aspect, the invention provides a method of assessing a cancercomprising detecting a level of one or more circulating biomarkers in asample from a subject selected from the group consisting of CD9, HSP70,Gal3, MIS, EGFR, ER, ICB3, CD63, B7H4, MUC1, DLL4, CD81, ERB3, VEGF,BCA225, BRCA, CA125, CD174, CD24, ERB2, NGAL, GPR30, CYFRA21, CD31,cMET, MUC2 or ERB4. CD9, HSP70, Gal3, MIS, EGFR, ER, ICB3, CD63, B7H4,MUC1, DLL4, CD81, ERB3, VEGF, BCA225, BRCA, BCA200, CA125, CD174, CD24,ERB2, NGAL, GPR30, CYFRA21, CD31, cMET, MUC2 or ERB4. In anotherembodiment, the one or more circulating biomarkers are selected from thegroup consisting of CD9, EphA2, EGFR, B7H3, PSMA, PCSA, CD63, STEAP,STEAP, CD81, B7H3, STEAP1, ICAM1 (CD54), PSMA, A33, DR3, CD66e, MFG-8e,EphA2, Hepsin, TMEM211, EphA2, TROP-2, EGFR, Mammoglobin, Hepsin,NPGP/NPFF2, PSCA, 5T4, NGAL, NK-2, EpCam, NGAL, NK-1R, PSMA, 5T4, PAI-1,and CD45. In still another embodiment, the one or more circulatingbiomarkers are selected from the group consisting of CD9, MIS Rii, ER,CD63, MUC1, HER3, STAT3, VEGFA, BCA, CA125, CD24, EPCAM, and ERB B4. Anynumber of useful biomarkers can be assessed from these groups, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In some embodiments, the one or morebiomarkers are one or more of Gal3, BCA200, OPN and NCAM, e.g., Gal3 andBCA200, OPN and NCAM, or all four. Assessing the cancer may comprisediagnosing, prognosing or theranosing the cancer. The cancer can be abreast cancer. The markers can be associated with a vesicle or vesiclepopulation. For example, the one or more circulating biomarker can be avesicle surface antigen or vesicle payload. Vesicle surface antigens canfurther be used as capture antigens, detector antigens, or both.

The invention further provides a method for predicting a response to atherapeutic agent comprising detecting a level of one or morecirculating biomarkers in a sample from a subject selected from thegroup consisting of CD9, HSP70, Gal3, MIS, EGFR, ER, ICB3, CD63, B7H4,MUC1, DLL4, CD81, ERB3, VEGF, BCA225, BRCA, CA125, CD174, CD24, ERB2,NGAL, GPR30, CYFRA21, CD31, cMET, MUC2 or ERB4. Biomarkers can also beselected from the group consisting of CD9, EphA2, EGFR, B7H3, PSMA,PCSA, CD63, STEAP, STEAP, CD81, B7H3, STEAP1, ICAM1 (CD54), PSMA, A33,DR3, CD66e, MFG-8e, EphA2, Hepsin, TMEM211, EphA2, TROP-2, EGFR,Mammoglobin, Hepsin, NPGP/NPFF2, PSCA, 5T4, NGAL, NK-2, EpCam, NGAL,NK-1R, PSMA, 5T4, PAI-1, and CD45. In still another embodiment, the oneor more circulating biomarkers are selected from the group consisting ofCD9, MIS Rii, ER, CD63, MUC1, HER3, STAT3, VEGFA, BCA, CA125, CD24,EPCAM, and ERB B4. Any number of useful biomarkers can be assessed fromthese groups, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In someembodiments, the one or more biomarkers are one or more of Gal3, BCA200,OPN and NCAM, e.g., Gal3 and BCA200, OPN and NCAM, or all four. Thetherapeutic agent can be a therapeutic agent for treating cancer. Thecancer can be a breast cancer. The markers can be associated with avesicle or vesicle population. For example, the one or more circulatingbiomarker can be a vesicle surface antigen or vesicle payload. Vesiclesurface antigens can further be used as capture antigens, detectorantigens, or both.

Various methods or platforms can be used to assess or detect biomarkersidentified herein. Examples of such methods or platforms include but arenot limited to using an antibody array, microbeads, or other methoddisclosed herein or known in the art. For example, a capture antibody oraptamer to the one or more biomarkers can be bound to the array or bead.The captured vesicles can then be detected using a detectable agent. Insome embodiments, captured vesicles are detected using an agent, e.g.,an antibody or aptamer, that recognizes general vesicle biomarkers thatdetect the overall population of vesicles, such as a tetraspanin orMFG-E8. These can include tetraspanins such as CD9, CD63 and/or CD81. Inother embodiments, the captured vesicles are detected using markersspecific for vesicle origin, e.g., a type of tissue or organ. In someembodiments, the captured vesicles are detected using CD31, a marker forcells or vesicles of endothelial origin. As desired, the biomarkers usedfor capture can also be used for detection, and vice versa.

Methods of the invention can be used to assess various diseases orconditions, where biomarkers correspond to various such diseases orconditions. For example, methods of the invention are applied to assessone or more cancers, such as those disclosed herein, wherein a methodcomprises detecting a level of one or more circulating biomarker in asample from a subject selected from the group consisting of 5T4(trophoblast), ADAM10, AGER/RAGE, APC, APP (β-amyloid), ASPH (A-10),B7H3 (CD276), BACE1, BAI3, BRCA1, BDNF, BIRC2, C1GALT1, CA125 (MUC16),Calmodulin 1, CCL2 (MCP-1), CD9, CD10, CD127 (IL7R), CD174, CD24, CD44,CD63, CD81, CEA, CRMP-2, CXCR3, CXCR4, CXCR6, CYFRA 21, derlin 1, DLL4,DPP6, E-CAD, EpCaM, EphA2 (H-77), ER(1) ESR1 α, ER(2) ESR2 β, Erb B4,Erbb2, erb3 (Erb-B3), PA2G4, FRT (FLT1), Gal3, GPR30 (G-coupled ER1),HAP1, HER3, HSP-27, HSP70, IC3b, IL8, insig, junction plakoglobin,Keratin 15, KRAS, Mammaglobin, MART1, MCT2, MFGE8, MMP9, MRP8, Muc1,MUC17, MUC2, NCAM, NG2 (CSPG4), Nga1, NHE-3, NT5E (CD73), ODC1, OPG,OPN, p53, PARK7, PCSA, PGP9.5 (PARKS), PR(B), PSA, PSMA, RAGE, STXBP4,Survivin, TFF3 (secreted), TIMP1, TIMP2, TMEM211, TRAF4 (scaffolding),TRAIL-R2 (death Receptor 5), TrkB, Tsg 101, UNC93a, VEGF A, VEGFR2,YB-1, VEGFR1, GCDPF-15 (PIP), BigH3 (TGFb1-induced protein), 5HT2B(serotonin receptor 2B), BRCA2, BACE 1, CDH1-cadherin. The methods cancomprise detecting protein, RNA or DNA of the specified targetbiomarker. The one or more marker can be assessed directly from abiological fluid, such as those fluids disclosed herein, or can beassessed for its association with a vesicle, e.g., as a vesicle surfaceantigen or as vesicle payload (e.g., soluble protein, mRNA or DNA). Aparticular biosignature determined using methods and compositions of theinvention can comprise any number of useful biomarkers, e.g., abiosignature can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or moredifferent biomarkers (or in some cases different molecules of the samebiomarkers, such protein and nucleic acid). Vesicle surface antigens canalso be used as capture antigens, detector antigens, or both, asdisclosed herein or in applications incorporated by reference.

Methods and compositions of the invention are applied to assess variousaspects of a cancer, including identifying different informative aspectsof a cancer, e.g., identifying a biosignature that is indicative ofmetastasis, angiogenesis, or classifying different stages, classes orsubclasses of the same tumor or tumor lineage.

Furthermore, methods of the invention comprise determining if a diseaseor condition affects immunomodulation in a subject. For example, the oneor more circulating biomarker for immunomodulation can be one or more ofCD45, FasL, CTLA4, CD80 and CD83. The one or more circulating biomarkerfor metastatis can be one or more of Muc1, CD147, TIMP1, TIMP2, MMP7,and MMP9. The one or more circulating biomarker for angiogenesis can beone or more of HIF2a, Tie2, Ang1, DLL4 and VEGFR2. Any number of usefulbiomarkers can be assessed from the groups, e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, 10 or more. The cancer can be a breast cancer. The markers can beassociated with a vesicle or vesicle population. For example, the one ormore circulating biomarker can be a vesicle surface antigen or vesiclepayload. Vesicle surface antigens can further be used as captureantigens, detector antigens, or both.

A biosignature can comprise DLL4 or cMET. Delta-like 4 (DLL4) is aNotch-ligand and is up-regulated during angiogenesis. cMET (alsoreferred to as c-Met, MET, or MNNG HOS Transforming gene) is aproto-oncogene that encodes a membrane receptor tyrosine kinase whoseligand is hepatocyte growth factor (HGF). The MET protein is sometimesreferred to as the hepatocyte growth factor receptor (HGFR). MET isnormally expressed on epithelial cells, and improper activation cantrigger tumor growth, angiogenesis and metastasis. DLL4 and cMET can beused as biomarkers to detect a vesicle population.

Biomarkers that can be derived and analyzed from a vesicle include miRNA(miR), miRNA*nonsense (miR*), and other RNAs (including, but not limitedto, mRNA, preRNA, priRNA, hnRNA, snRNA, siRNA, shRNA). A miRNA biomarkercan include not only its miRNA and microRNA* nonsense, but its precursormolecules: pri-microRNAs (pri-miRs) and pre-microRNAs (pre-miRs). Thesequence of a miRNA can be obtained from publicly available databasessuch as http://www.mirbase.org/, http://www.microrna.org/, or any othersavailable. Unless noted, the terms miR, miRNA and microRNA are usedinterchangeably throughout unless noted. In some embodiments, themethods of the invention comprise isolating vesicles, and assessing themiRNA payload within the isolated vesicles. The biomarker can also be anucleic acid molecule (e.g. DNA), protein, or peptide. The presence orabsence, expression level, mutations (for example genetic mutations,such as deletions, translocations, duplications, nucleotide or aminoacid substitutions, and the like) can be determined for the biomarker.Any epigenetic modulation or copy number variation of a biomarker canalso be analyzed.

The one or more biomarkers analyzed can be indicative of a particulartissue or cell of origin, disease, or physiological state. Furthermore,the presence, absence or expression level of one or more of thebiomarkers described herein can be correlated to a phenotype of asubject, including a disease, condition, prognosis or drug efficacy. Thespecific biomarker and biosignature set forth below constitutenon-inclusive examples for each of the diseases, condition comparisons,conditions, and/or physiological states. Furthermore, the one or morebiomarker assessed for a phenotype can be a cell-of-origin specificvesicle.

The one or more miRNAs used to characterize a phenotype may be selectedfrom those disclosed in PCT Publication No. WO2009/036236. For example,one or more miRNAs listed in Tables I-VI (FIGS. 6-11) therein can beused to characterize colon adenocarcinoma, colorectal cancer, prostatecancer, lung cancer, breast cancer, b-cell lymphoma, pancreatic cancer,diffuse large BCL cancer, CLL, bladder cancer, renal cancer,hypoxia-tumor, uterine leiomyomas, ovarian cancer, hepatitis Cvirus-associated hepatocellular carcinoma, ALL, Alzheimer's disease,myelofibrosis, myelofibrosis, polycythemia vera, thrombocythemia, HIV,or HIV-I latency, as further described herein.

The one or more miRNAs can be detected in a vesicle. The one or moremiRNAs can be miR-223, miR-484, miR-191, miR-146a, miR-016, miR-026a,miR-222, miR-024, miR-126, and miR-32. One or more miRNAs can also bedetected in PBMC. The one or more miRNAs can be miR-223, miR-150,miR-146b, miR-016, miR-484, miR-146a, miR-191, miR-026a, miR-019b, ormiR-020a. The one or more miRNAs can be used to characterize aparticular disease or condition. For example, for the disease bladdercancer, one or more miRNAs can be detected, such as miR-223, miR-26b,miR-221, miR-103-1, miR-185, miR-23b, miR-203, miR-17-5p, miR-23a,miR-205 or any combination thereof. The one or more miRNAs may beupregulated or overexpressed.

In some embodiments, the one or more miRNAs is used to characterizehypoxia-tumor. The one or more miRNA may be miR-23, miR-24, miR-26,miR-27, miR-103, miR-107, miR-181, miR-210, or miR-213, and may beupregulated. One or more miRNAs can also be used to characterize uterineleiomyomas. For example, the one or more miRNAs used to characterize auterine leiomyoma may be a let-7 family member, miR-21, miR-23b,miR-29b, or miR-197. The miRNA can be upregulated.

Myelofibrosis can also be characterized by one or more miRNAs, such asmiR-190, which can be upregulated; miR-31, miR-150 and miR-95, which canbe downregulated, or any combination thereof. Furthermore,myelofibrosis, polycythemia vera or thrombocythemia can also becharacterized by detecting one or more miRNAs, such as, but not limitedto, miR-34a, miR-342, miR-326, miR-105, miR-149, miR-147, or anycombination thereof. The one or more miRNAs may be down-regulated.

Other examples of phenotypes that can be characterized by assessing avesicle for one or more biomarkers are further described herein.

The one or more biomarkers can be detected using a probe. A probe cancomprise an oligonucleotide, such as DNA or RNA, an aptamer, monoclonalantibody, polyclonal antibody, Fabs, Fab′, single chain antibody,synthetic antibody, peptoid, zDNA, peptide nucleic acid (PNA), lockednucleic acid (LNA), lectin, synthetic or naturally occurring chemicalcompound (including but not limited to a drug or labeling reagent),dendrimer, or a combination thereof. The probe can be directly detected,for example by being directly labeled, or be indirectly detected, suchas through a labeling reagent. The probe can selectively recognize abiomarker. For example, a probe that is an oligonucleotide canselectively hybridize to a miRNA biomarker.

In aspects, the invention provides for the diagnosis, theranosis,prognosis, disease stratification, disease staging, treatment monitoringor predicting responder/non-responder status of a disease or disorder ina subject. The invention comprises assessing vesicles from a subject,including assessing biomarkers present on the vesicles and/or assessingpayload within the vesicles, such as protein, nucleic acid or otherbiological molecules. Any appropriate biomarker that can be assessedusing a vesicle and that relates to a disease or disorder can be usedthe carry out the methods of the invention. Furthermore, any appropriatetechnique to assess a vesicle as described herein can be used. Exemplarybiomarkers for specific diseases that can be assessed according to themethods of the invention include the biomarkers described inInternational Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein.

Any of the types of biomarkers or specific biomarkers described hereincan be assessed to identify a biosignature or to identify a candidatebiosignature. Exemplary biomarkers include without limitation those inTable 5. The markers in the table can be used for capture and/ordetection of vesicles for characterizing phenotypes as disclosed herein.In some cases, multiple capture and/or detectors are used to enhance thecharacterization. The markers can be detected as protein or as mRNA,which can be circulating freely or in a complex with other biologicalmolecules. The markers can be detected as vesicle surface antigens orand vesicle payload. The “Illustrative Class” indicates indications forwhich the markers are known markers. Those of skill will appreciate thatthe markers can also be used in alternate settings in certain instances.For example, a marker which can be used to characterize one type diseasemay also be used to characterize another disease as appropriate.Consider a non-limiting example of a tumor marker which can be used as abiomarker for tumors from various lineages.

TABLE 5 Illustrative Vesicle Associated Biomarkers Illustrative ClassBiomarkers Drug associated ABCC1, ABCG2, ACE2, ADA, ADH1C, ADH4, AGT,AR, AREG, ASNS, targets and BCL2, BCRP, BDCA1, beta III tubulin, BIRC5,B-RAF, BRCA1, BRCA2, CA2, prognostic markers caveolin, CD20, CD25, CD33,CD52, CDA, CDKN2A, CDKN1A, CDKN1B, CDK2, CDW52, CES2, CK 14, CK 17, CK5/6, c-KIT, c-Met, c-Myc, COX-2, Cyclin D1, DCK, DHFR, DNMT1, DNMT3A,DNMT3B, E-Cadherin, ECGF1, EGFR, EML4-ALK fusion, EPHA2, Epiregulin, ER,ERBR2, ERCC1, ERCC3, EREG, ESR1, FLT1, folate receptor, FOLR1, FOLR2,FSHB, FSHPRH1, FSHR, FYN, GART, GNA11, GNAQ, GNRH1, GNRHR1, GSTP1, HCK,HDAC1, hENT-1, Her2/Neu, HGF, HIF1A, HIG1, HSP90, HSP90AA1, HSPCA,IGF-1R, IGFRBP, IGFRBP3, IGFRBP4, IGFRBP5, IL13RA1, IL2RA, KDR, Ki67,KIT, K-RAS, LCK, LTB, Lymphotoxin Beta Receptor, LYN, MET, MGMT, MLH1,MMR, MRP1, MS4A1, MSH2, MSH5, Myc, NFKB1, NFKB2, NFKBIA, NRAS, ODC1,OGFR, p16, p21, p27, p53, p95, PARP-1, PDGFC, PDGFR, PDGFRA, PDGFRB,PGP, PGR, PI3K, POLA, POLA1, PPARG, PPARGC1, PR, PTEN, PTGS2, PTPN12,RAF1, RARA, ROS1, RRM1, RRM2, RRM2B, RXRB, RXRG, SIK2, SPARC, SRC,SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, Survivin, TK1, TLE3, TNF, TOP1,TOP2A, TOP2B, TS, TUBB3, TXN, TXNRD1, TYMS, VDR, VEGF, VEGFA, VEGFC,VHL, YES1, ZAP70 Cancer treatment AR, AREG (Amphiregulin), BRAF, BRCA1,cKIT, cMET, EGFR, EGFR associated markers w/T790M, EML4-ALK, ER, ERBB3,ERBB4, ERCC1, EREG, GNA11, GNAQ, hENT-1, Her2, Her2 Exon 20 insert,IGF1R, Ki67, KRAS, MGMT, MGMT methylation, MSH2, MSI, NRAS, PGP (MDR1),PIK3CA, PR, PTEN, ROS1, ROS1 translocation, RRM1, SPARC, TLE3, TOPO1,TOPO2A, TS, TUBB3, VEGFR2 Cancer treatment AR, AREG, BRAF, BRCA1, cKIT,cMET, EGFR, EGFR w/T790M, EML4- associated markers ALK, ER, ERBB3,ERBB4, ERCC1, EREG, GNA11, GNAQ, Her2, Her2 Exon 20 insert, IGFR1, Ki67,KRAS, MGMT-Me, MSH2, MSI, NRAS, PGP (MDR-1), PIK3CA, PR, PTEN, ROS1translocation, RRM1, SPARC, TLE3, TOPO1, TOPO2A, TS, TUBB3, VEGFR2 Coloncancer AREG, BRAF, EGFR, EML4-ALK, ERCC1, EREG, KRAS, MSI, NRAS,treatment associated PIK3CA, PTEN, TS, VEGFR2 markers Colon cancer AREG,BRAF, EGFR, EML4-ALK, ERCC1, EREG, KRAS, MSI, NRAS, treatment associatedPIK3CA, PTEN, TS, VEGFR2 markers Melanoma treatment BRAF, cKIT, ERBB3,ERBB4, ERCC1, GNA11, GNAQ, MGMT, MGMT associated markers methylation,NRAS, PIK3CA, TUBB3, VEGFR2 Melanoma treatment BRAF, cKIT, ERBB3, ERBB4,ERCC1, GNA11, GNAQ, MGMT-Me, NRAS, associated markers PIK3CA, TUBB3,VEGFR2 Ovarian cancer BRCA1, cMET, EML4-ALK, ER, ERBB3, ERCC1, hENT-1,HER2, IGF1R, treatment associated PGP(MDR1), PIK3CA, PR, PTEN, RRM1,TLE3, TOPO1, TOPO2A, TS markers Ovarian cancer BRCA1, cMET, EML4-ALK(translocation), ER, ERBB3, ERCC1, HER2, treatment associated PIK3CA,PR, PTEN, RRM1, TLE3, TS markers Breast cancer BRAF, BRCA1, EGFR, EGFRT790M, EML4-ALK, ER, ERBB3, ERCC1, treatment associated HER2, Ki67, PGP(MDR1), PIK3CA, PR, PTEN, ROS1, ROS1 translocation, markers RRM1, TLE3,TOPO1, TOPO2A, TS Breast cancer BRAF, BRCA1, EGFR w/T790M, EML4-ALK, ER,ERBB3, ERCC1, HER2, treatment associated Ki67, KRAS, PIK3CA, PR, PTEN,ROS1 translocation, RRM1, TLE3, TOPO1, markers TOPO2A, TS NSCLC cancerBRAF, BRCA1, cMET, EGFR, EGFR w/T790M, EML4-ALK, ERCC1, Her2 treatmentassociated Exon 20 insert, KRAS, MSH2, PIK3CA, PTEN, ROS1 (trans), RRM1,TLE3, TS, markers VEGFR2 NSCLC cancer BRAF, cMET, EGFR, EGFR w/T790M,EML4-ALK, ERCC1, Her2 Exon 20 treatment associated insert, KRAS, MSH2,PIK3CA, PTEN, ROS1 translocation, RRM1, TLE3, TS markers Cancer/AngioErb 2, Erb 3, Erb 4, UNC93a, B7H3, MUC1, MUC2, MUC16, MUC17, 5T4, RAGE,VEGFA, VEGFR2, FLT1, DLL4, Epcam Tissue (Breast) BIG H3, GCDFP-15,PR(B), GPR 30, CYFRA 21, BRCA 1, BRCA 2, ESR 1, ESR2 Tissue (Prostate)PSMA, PCSA, PSCA, PSA, TMPRSS2 Inflammation/Immune MFG-E8, IFNAR, CD40,CD80, MICB, HLA-DRb, IL-17-Ra Common vesicle HSPA8, CD63, Actb, GAPDH,CD9, CD81, ANXA2, HSP90AA1, ENO1, markers YWHAZ, PDCD6IP, CFL1, SDCBP,PKN2, MSN, MFGE8, EZR, YWHAG, PGK1, EEF1A1, PPIA, GLC1F, GK, ANXA6,ANXA1, ALDOA, ACTG1, TPI1, LAMP2, HSP90AB1, DPP4, YWHAB, TSG101, PFN1,LDHB, HSPA1B, HSPA1A, GSTP1, GNAI2, GDI2, CLTC, ANXA5, YWHAQ, TUBA1A,THBS1, PRDX1, LDHA, LAMP1, CLU, CD86 Common vesicle CD63, GAPDH, CD9,CD81, ANXA2, ENO1, SDCBP, MSN, MFGE8, EZR, membrane markers GK, ANXA1,LAMP2, DPP4, TSG101, HSPA1A, GDI2, CLTC, LAMP1, CD86, ANPEP, TFRC,SLC3A2, RDX, RAP1B, RAB5C, RAB5B, MYH9, ICAM1, FN1, RAB11B, PIGR,LGALS3, ITGB1, EHD1, CLIC1, ATP1A1, ARF1, RAP1A, P4HB, MUC1, KRT10,HLA-A, FLOT1, CD59, C1orf58, BASP1, TACSTD1, STOM Common vesicle MHCclass I, MHC class II, Integrins, Alpha 4 beta 1, Alpha M beta 2, Beta2, markers ICAM1/CD54, P-selection, Dipeptidylpeptidase IV/CD26,Aminopeptidase n/CD13, CD151, CD53, CD37, CD82, CD81, CD9, CD63, Hsp70,Hsp84/90 Actin, Actin-binding proteins, Tubulin, Annexin I, Annexin II,Annexin IV, Annexin V, Annexin VI, RAB7/RAP1B/RADGDI, Gi2alpha/14-3-3,CBL/LCK, CD63, GAPDH, CD9, CD81, ANXA2, ENO1, SDCBP, MSN, MFGE8, EZR,GK, ANXA1, LAMP2, DPP4, TSG101, HSPA1A, GDI2, CLTC, LAMP1, Cd86, ANPEP,TFRC, SLC3A2, RDX, RAP1B, RAB5C, RAB5B, MYH9, ICAM1, FN1, RAB11B, PIGR,LGALS3, ITGB1, EHD1, CLIC1, ATP1A1, ARF1, RAP1A, P4HB, MUC1, KRT10,HLA-A, FLOT1, CD59, C1orf58, BASP1, TACSTD1, STOM Vesicle markers A33,a33 n15, AFP, ALA, ALIX, ALP, AnnexinV, APC, ASCA, ASPH (246-260), ASPH(666-680), ASPH (A-10), ASPH (D01P), ASPH (D03), ASPH (G- 20), ASPH(H-300), AURKA, AURKB, B7H3, B7H4, BCA-225, BCNP, BDNF, BRCA, CA125(MUC16), CA-19-9, C-Bir, CD1.1, CD10, CD174 (Lewis y), CD24, CD44, CD46,CD59 (MEM-43), CD63, CD66e CEA, CD73, CD81, CD9, CDA, CDAC11a2, CEA,C-Erb2, C-erbB2, CRMP-2, CRP, CXCL12, CYFRA21-1, DLL4, DR3, EGFR, Epcam,EphA2, EphA2 (H-77), ER, ErbB4, EZH2, FASL, FRT, FRT c.f23, GDF15, GPCR,GPR30, Gro-alpha, HAP, HBD1, HBD2, HER 3 (ErbB3), HSP, HSP70, hVEGFR2,iC3b, IL 6 Unc, IL-1B, IL6 Unc, IL6R, IL8, IL-8, INSIG-2, KLK2, L1CAM,LAMN, LDH, MACC-1, MAPK4, MART-1, MCP-1, M-CSF, MFG-E8, MIC1, MIF, MISRII, MMG, MMP26, MMP7, MMP9, MS4A1, MUC1, MUC1 seq1, MUC1 seq11A, MUC17,MUC2, Ncam, NGAL, NPGP/NPFF2, OPG, OPN, p53, p53, PA2G4, PBP, PCSA,PDGFRB, PGP9.5, PIM1, PR (B), PRL, PSA, PSMA, PSME3, PTEN, R5- CD9 Tube1, Reg IV, RUNX2, SCRN1, seprase, SERPINB3, SPARC, SPB, SPDEF, SRVN,STAT 3, STEAP1, TF (FL-295), TFF3, TGM2, TIMP-1, TIMP1, TIMP2, TMEM211,TMPRSS2, TNF-alpha, Trail-R2, Trail-R4, TrKB, TROP2, Tsg 101, TWEAK,UNC93A, VEGF A, YPSMA-1 Vesicle markers NSE, TRIM29, CD63, CD151, ASPH,LAMP2, TSPAN1, SNAIL, CD45, CKS1, NSE, FSHR, OPN, FTH1, PGP9, ANNEXIN 1,SPD, CD81, EPCAM, PTH1R, CEA, CYTO 7, CCL2, SPA, KRAS, TWIST1, AURKB,MMP9, P27, MMP1, HLA, HIF, CEACAM, CENPH, BTUB, INTG b4, EGFR, NACC1,CYTO 18, NAP2, CYTO 19, ANNEXINV, TGM2, ERB2, BRCA1, B7H3, SFTPC, PNT,NCAM, MS4A1, P53, INGA3, MUC2, SPA, OPN, CD63, CD9, MUC1, UNCR3, PANADH, HCG, TIMP, PSMA, GPCR, RACK1, PSCA, VEGF, BMP2, CD81, CRP, PROGRP,B7H3, MUC1, M2PK, CD9, PCSA, PSMA Vesicle markers TFF3, MS4A1, EphA2,GAL3, EGFR, N-gal, PCSA, CD63, MUC1, TGM2, CD81, DR3, MACC-1, TrKB,CD24, TIMP-1, A33, CD66 CEA, PRL, MMP9, MMP7, TMEM211, SCRN1, TROP2,TWEAK, CDACC1, UNC93A, APC, C- Erb, CD10, BDNF, FRT, GPR30, P53, SPR,OPN, MUC2, GRO-1, tsg 101, GDF15 Vesicle markers CD9, Erb2, Erb4, CD81,Erb3, MUC16, CD63, DLL4, HLA-Drpe, B7H3, IFNAR, 5T4, PCSA, MICB, PSMA,MFG-E8, Muc1, PSA, Muc2, Unc93a, VEGFR2, EpCAM, VEGF A, TMPRSS2, RAGE,PSCA, CD40, Muc17, IL-17- RA, CD80 Benign Prostate BCMA, CEACAM-1, HVEM,IL-1 R4, IL-10 Rb, Trappin-2, p53, hsa-miR-329, Hyperplasia (BPH)hsa-miR-30a, hsa-miR-335, hsa-miR-152, hsa-miR-151-5p, hsa-miR-200a,hsa- miR-145, hsa-miR-29a, hsa-miR-106b, hsa-miR-595, hsa-miR-142-5p,hsa-miR- 99a, hsa-miR-20b, hsa-miR-373, hsa-miR-502-5p, hsa-miR-29b,hsa-miR-142-3p, hsa-miR-663, hsa-miR-423-5p, hsa-miR-15a, hsa-miR-888,hsa-miR-361-3p, hsa- miR-365, hsa-miR-10b, hsa-miR-199a-3p,hsa-miR-181a, hsa-miR-19a, hsa-miR- 125b, hsa-miR-760, hsa-miR-7a,hsa-miR-671-5p, hsa-miR-7c, hsa-miR-1979, hsa-miR-103 MetastaticProstate hsa-miR-100, hsa-miR-1236, hsa-miR-1296, hsa-miR-141,hsa-miR-146b-5p, hsa- Cancer miR-17*, hsa-miR-181a, hsa-miR-200b,hsa-miR-20a*, hsa-miR-23a*, hsa-miR- 331-3p, hsa-miR-375, hsa-miR-452,hsa-miR-572, hsa-miR-574-3p, hsa-miR-577, hsa-miR-582-3p, hsa-miR-937,miR-10a, miR-134, miR-141, miR-200b, miR-30a, miR-32, miR-375, miR-495,miR-564, miR-570, miR-574-3p, miR-885-3p Metastatic Prostatehsa-miR-200b, hsa-miR-375, hsa-miR-141, hsa-miR-331-3p, hsa-miR-181a,hsa- Cancer miR-574-3p Prostate Cancer hsa-miR-574-3p, hsa-miR-141,hsa-miR-432, hsa-miR-326, hsa-miR-2110, hsa- miR-181a-2*, hsa-miR-107,hsa-miR-301a, hsa-miR-484, hsa-miR-625* Metastatic Prostatehsa-miR-582-3p, hsa-miR-20a*, hsa-miR-375, hsa-miR-200b, hsa-miR-379,hsa- Cancer miR-572, hsa-miR-513a-5p, hsa-miR-577, hsa-miR-23a*,hsa-miR-1236, hsa- miR-609, hsa-miR-17*, hsa-miR-130b, hsa-miR-619,hsa-miR-624*, hsa-miR-198 Metastatic Prostate FOX01A, SOX9, CLNS1A,PTGDS, XPO1, LETMD1, RAD23B, ABCC3, APC, Cancer CHES1, EDNRA, FRZB,HSPG2, TMPRSS2_ETV1 fusion Prostate Cancer hsa-let-7b, hsa-miR-107,hsa-miR-1205, hsa-miR-1270, hsa-miR-130b, hsa-miR- 141, hsa-miR-143,hsa-miR-148b*, hsa-miR-150, hsa-miR-154*, hsa-miR-181a*,hsa-miR-181a-2*, hsa-miR-18a*, hsa-miR-19b-1*, hsa-miR-204,hsa-miR-2110, hsa-miR-215, hsa-miR-217, hsa-miR-219-2-3p, hsa-miR-23b*,hsa-miR-299-5p, hsa-miR-301a, hsa-miR-301a, hsa-miR-326, hsa-miR-331-3p,hsa-miR-365*, hsa- miR-373*, hsa-miR-424, hsa-miR-424*, hsa-miR-432,hsa-miR-450a, hsa-miR- 451, hsa-miR-484, hsa-miR-497, hsa-miR-517*,hsa-miR-517a, hsa-miR-518f, hsa-miR-574-3p, hsa-miR-595, hsa-miR-617,hsa-miR-625*, hsa-miR-628-5p, hsa-miR-629, hsa-miR-634, hsa-miR-769-5p,hsa-miR-93, hsa-miR-96 Prostate Cancer CD9, PSMA, PCSA, CD63, CD81,B7H3, IL 6, OPG-13, IL6R, PA2G4, EZH2, RUNX2, SERPINB3, EpCam ProstateCancer A33, a33 n15, AFP, ALA, ALIX, ALP, AnnexinV, APC, ASCA, ASPH(246-260), ASPH (666-680), ASPH (A-10), ASPH (D01P), ASPH (D03), ASPH(G- 20), ASPH (H-300), AURKA, AURKB, B7H3, B7H4, BCA-225, BCNP, BDNF,BRCA, CA125 (MUC16), CA-19-9, C-Bir, CD1.1, CD10, CD174 (Lewis y), CD24,CD44, CD46, CD59 (MEM-43), CD63, CD66e CEA, CD73, CD81, CD9, CDA, CDAC11a2, CEA, C-Erb2, C-erbB2, CRMP-2, CRP, CXCL12, CYFRA21-1, DLL4, DR3,EGFR, Epcam, EphA2, EphA2 (H-77), ER, ErbB4, EZH2, FASL, FRT, FRT c.f23,GDF15, GPCR, GPR30, Gro-alpha, HAP, HBD 1, HBD2, HER 3 (ErbB3), HSP,HSP70, hVEGFR2, iC3b, IL 6 Unc, IL-1B, IL6 Unc, IL6R, IL8, IL-8,INSIG-2, KLK2, L1CAM, LAMN, LDH, MACC-1, MAPK4, MART-1, MCP-1, M-CSF,MFG-E8, MIC1, MIF, MIS RII, MMG, MMP26, MMP7, MMP9, MS4A1, MUC1, MUC1seq1, MUC1 seq11A, MUC17, MUC2, Ncam, NGAL, NPGP/NPFF2, OPG, OPN, p53,p53, PA2G4, PBP, PCSA, PDGFRB, PGP9.5, PIM1, PR (B), PRL, PSA, PSMA,PSME3, PTEN, R5- CD9 Tube 1, Reg IV, RUNX2, SCRN1, seprase, SERPINB3,SPARC, SPB, SPDEF, SRVN, STAT 3, STEAP1, TF (FL-295), TFF3, TGM2,TIMP-1, TIMP1, TIMP2, TMEM211, TMPRSS2, TNF-alpha, Trail-R2, Trail-R4,TrKB, TROP2, Tsg 101, TWEAK, UNC93A, VEGF A, YPSMA-1 Prostate Cancer5T4, ACTG1, ADAM10, ADAM15, ALDOA, ANXA2, ANXA6, APOA1, Vesicle MarkersATP1A1, BASP1, C1orf58, C20orf114, C8B, CAPZA1, CAV1, CD151, CD2AP,CD59, CD9, CD9, CFL1, CFP, CHMP4B, CLTC, COTL1, CTNND1, CTSB, CTSZ,CYCS, DPP4, EEF 1A1, EHD1, ENO1, F11R, F2, F5, FAM125A, FNBP1L, FOLH1,GAPDH, GLB1, GPX3, HIST1H1C, HIST1H2AB, HSP90AB1, HSPA1B, HSPA8, IGSF8,ITGB1, ITIH3, JUP, LDHA, LDHB, LUM, LYZ, MFGE8, MGAM, MMP9, MYH2, MYL6B,NME1, NME2, PABPC1, PABPC4, PACSIN2, PCBP2, PDCD6IP, PRDX2, PSA, PSMA,PSMA1, PSMA2, PSMA4, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMB4, PSMB5,PSMB6, PSMB8, PTGFRN, RPS27A, SDCBP, SERINC5, SH3GL1, SLC3A2, SMPDL3B,SNX9, TACSTD1, TCN2, THBS1, TPI1, TSG101, TUBB, VDAC2, VPS37B, YWHAG,YWHAQ, YWHAZ Prostate Cancer FLNA, DCRN, HER 3 (ErbB3), VCAN, CD9, GAL3,CDADC1, GM-CSF, Vesicle Markers EGFR, RANK, CSA, PSMA, ChickenIgY, B7H3,PCSA, CD63, CD3, MUC1, TGM2, CD81, S100-A4, MFG-E8, Integrin,NK-2R(C-21), PSA, CD24, TIMP-1, IL6 Unc, PBP, PIM1, CA-19-9, Trail-R4,MMP9, PRL, EphA2, TWEAK, NY- ESO-1, Mammaglobin, UNC93A, A33, AURKB,CD41, XAGE-1, SPDEF, AMACR, seprase/FAP, NGAL, CXCL12, FRT, CD66e CEA,SIM2 (C-15), C- Bir, STEAP, PSIP1/LEDGF, MUC17, hVEGFR2, ERG, MUC2,ADAM10, ASPH (A-10), CA125, Gro-alpha, Tsg 101, SSX2, Trail-R4 ProstateCancer NT5E (CD73), A33, ABL2, ADAM10, AFP, ALA, ALIX, ALPL, AMACR, ApoVesicle Markers J/CLU, ASCA, ASPH (A-10), ASPH (D01P), AURKB, B7H3,B7H4, BCNP, BDNF, CA125 (MUC16), CA-19-9, C-Bir (Flagellin), CD10,CD151, CD24, CD3, CD41, CD44, CD46, CD59(MEM-43), CD63, CD66e CEA, CD81,CD9, CDA, CDADC1, C-erbB2, CRMP-2, CRP, CSA, CXCL12, CXCR3, CYFRA21- 1,DCRN, DDX-1, DLL4, EGFR, EpCAM, EphA2, ERG, EZH2, FASL, FLNA, FRT, GAL3,GATA2, GM-CSF, Gro-alpha, HAP, HER3 (ErbB3), HSP70, HSPB1, hVEGFR2,iC3b, IL-1B, IL6 R, IL6 Unc, IL7 R alpha/CD127, IL8, INSIG-2, Integrin,KLK2, Label, LAMN, Mammaglobin, M-CSF, MFG-E8, MIF, MIS RII, MMP7, MMP9,MS4A1, MUC1, MUC17, MUC2, Ncam, NDUFB7, NGAL, NK-2R(C-21), NY-ESO-1,p53, PBP, PCSA, PDGFRB, PIM1, PRL, PSA, PSIP1/LEDGF, PSMA, RAGE, RANK,Reg IV, RUNX2, S100-A4, seprase/FAP, SERPINB3, SIM2 (C-15), SPARC, SPC,SPDEF, SPP1, SSX2, SSX4, STEAP, STEAP4, TFF3, TGM2, TIMP-1, TMEM211,Trail-R2, Trail-R4, TrKB (poly), Trop2, Tsg 101, TWEAK, UNC93A, VCAN,VEGF A, wnt-5a(C- 16), XAGE, XAGE-1 Prostate Cancer hsa-miR-1974,hsa-miR-27b, hsa-miR-103, hsa-miR-146a, hsa-miR-22, hsa-miR- Treatment382, hsa-miR-23a, hsa-miR-376c, hsa-miR-335, hsa-miR-142-5p,hsa-miR-221, hsa-miR-142-3p, hsa-miR-151-3p, hsa-miR-21, hsa-miR-16Prostate Cancer let-7d, miR-148a, miR-195, miR-25, miR-26b, miR-329,miR-376c, miR-574-3p, miR-888, miR-9, miR1204, miR-16-2*, miR-497,miR-588, miR-614, miR-765, miR92b*, miR-938, let-7f-2*, miR-300,miR-523, miR-525-5p, miR-1182, miR- 1244, miR-520d-3p, miR-379, let-7b,miR-125a-3p, miR-1296, miR-134, miR- 149, miR-150, miR-187, miR-32,miR-324-3p, miR-324-5p, miR-342-3p, miR- 378, miR-378*, miR-384,miR-451, miR-455-3p, miR-485-3p, miR-487a, miR- 490-3p, miR-502-5p,miR-548a-5p, miR-550, miR-562, miR-593, miR-593*, miR-595, miR-602,miR-603, miR-654-5p, miR-877*, miR-886-5p, miR-125a-5p, miR-140-3p,miR-192, miR-196a, miR-2110, miR-212, miR-222, miR-224*, miR-30b*,miR-499-3p, miR-505* Prostate Cancer hsa-miR-451, hsa-miR-223,hsa-miR-593*, hsa-miR-1974, hsa-miR-486-5p, hsa- miR-19b, hsa-miR-320b,hsa-miR-92a, hsa-miR-21, hsa-miR-675*, hsa-miR-16, hsa-miR-876-5p,hsa-miR-144, hsa-miR-126, hsa-miR-137, hsa-miR-1913, hsa- miR-29b-1*,hsa-miR-15a, hsa-miR-93, hsa-miR-1266 Prostate Cancer miR-148a, miR-329,miR-9, miR-378*, miR-25, miR-614, miR-518c*, miR-378, miR-765,let-7f-2*, miR-574-3p, miR-497, miR-32, miR-379, miR-520g, miR- 542-5p,miR-342-3p, miR-1206, miR-663, miR-222 Prostate Cancer hsa-miR-877*,hsa-miR-593, hsa-miR-595, hsa-miR-300, hsa-miR-324-5p, hsa- miR-548a-5p,hsa-miR-329, hsa-miR-550, hsa-miR-886-5p, hsa-miR-603, hsa- miR-490-3p,hsa-miR-938, hsa-miR-149, hsa-miR-150, hsa-miR-1296, hsa-miR- 384,hsa-miR-487a, hsa-miRPlus-C1089, hsa-miR-485-3p, hsa-miR-525-5p ProstateCancer miR-588, miR-1258, miR-16-2*, miR-938, miR-526b, miR-92b*,let-7d, miR- 378*, miR-124, miR-376c, miR-26b, miR-1204, miR-574-3p,miR-195, miR-499- 3p, miR-2110, miR-888 Prostate (PCSA + miR-182,miR-663, miR-155, mirR-125a-5p, miR-548a-5p, miR-628-5p, miR- cMVs)517*, miR-450a, miR-920, hsa-miR-619, miR-1913, miR-224*, miR-502-5p,miR-888, miR-376a, miR-542-5p, miR-30b* and miR-1179 Prostate CancermiR-183-96-182 cluster (miRs-183, 96 and 182), metal ion transportersuch as hZIP1, SLC39A1, SLC39A2, SLC39A3, SLC39A4, SLC39A5, SLC39A6,SLC39A7, SLC39A8, SLC39A9, SLC39A10, SLC39A11, SLC39A12, SLC39A13,SLC39A14 Prostate Cancer RAD23B, FBP1, TNFRSF1A, CCNG2, NOTCH3, ETV1,BID, SIM2, LETMD1, ANXA1, miR-519d, and miR-647 Prostate Cancer RAD23B,FBP1, TNFRSF1A, NOTCH3, ETV1, BID, SIM2, ANXA1 and BCL2 Prostate CancerANPEP, ABL1, PSCA, EFNA1, HSPB1, INMT and TRIP13 Prostate Cancer E2F3,c-met, pRB, EZH2, e-cad, CAXII, CAIX, HIF-1α, Jagged, PIM-1, hepsin,RECK, Clusterin, MMP9, MTSP-1, MMP24, MMP15, IGFBP-2, IGFBP-3, E2F4,caveolin, EF-1A, Kallikrein 2, Kallikrein 3, PSGR Prostate Cancer A2ML1,BAX, C10orf47, C1orf162, CSDA, EIFC3, ETFB, GABARAPL2, GUK1, GZMH,HIST1H3B, HLA-A, HSP90AA1, NRGN, PRDX5, PTMA, RABAC1, RABAGAP1L, RPL22,SAP18, SEPW1, SOX1 Androgen Receptor GTF2F1, CTNNB1, PTEN, APPL1, GAPDH,CDC37, PNRC1, AES, UXT, RAN, (AR) pathway PA2G4, JUN, BAG1, UBE2I,HDAC1, COX5B, NCOR2, STUB1, HIPK3, PXN, members in cMVs NCOA4 EGFR1pathway RALBP1, SH3BGRL, RBBP7, REPS1, SNRPD2, CEBPB, APPL1, MAP3K3,members in cMVs EEF1A1, GRB2, RAC1, SNCA, MAP2K3, CEBPA, CDC42, SH3KBP1,CBL, PTPN6, YWHAB, FOXO1, JAK1, KRT8, RALGDS, SMAD2, VAV1, NDUFA13,PRKCB1, MYC, JUN, RFXANK, HDAC1, HIST3H3, PEBP1, PXN, TNIP1, PKN2TNF-alpha pathway BCL3, SMARCE1, RPS11, CDC37, RPL6, RPL8, PAPOLA,PSMC1, CASP3, members in cMVs AKT2, MAP3K7IP2, POLR2L, TRADD, SMARCA4,HIST3H3, GNB2L1, PSMD1, PEBP1, HSPB1, TNIP1, RPS13, ZFAND5, YWHAQ,COMMD1, COPS3, POLR1D, SMARCC2, MAP3K3, BIRC3, UBE2D2, HDAC2, CASP8,MCM7, PSMD7, YWHAG, NFKBIA, CAST, YWHAB, G3BP2, PSMD13, FBL, RELB,YWHAZ, SKP1, UBE2D3, PDCD2, HSP90AA1, HDAC1, KPNA2, RPL30, GTF2I, PFDN2Colorectal cancer CD9, EGFR, NGAL, CD81, STEAP, CD24, A33, CD66E, EPHA2,Ferritin, GPR30, GPR110, MMP9, OPN, p53, TMEM211, TROP2, TGM2, TIMP,EGFR, DR3, UNC93A, MUC17, EpCAM, MUC1, MUC2, TSG101, CD63, B7H3Colorectal cancer DR3, STEAP, epha2, TMEM211, unc93A, A33, CD24, NGAL,EpCam, MUC17, TROP2, TETS Colorectal cancer A33, AFP, ALIX, ALX4, ANCA,APC, ASCA, AURKA, AURKB, B7H3, BANK1, BCNP, BDNF, CA-19-9, CCSA-2,CCSA-3&4, CD10, CD24, CD44, CD63, CD66 CEA, CD66e CEA, CD81, CD9, CDA,C-Erb2, CRMP-2, CRP, CRTN, CXCL12, CYFRA21-1, DcR3, DLL4, DR3, EGFR,Epcam, EphA2, FASL, FRT, GAL3, GDF15, GPCR (GPR110), GPR30, GRO-1, HBD1, HBD2, HNP1-3, IL-1B, IL8, IMP3, L1CAM, LAMN, MACC-1, MGC20553, MCP-1,M- CSF, MIC1, MIF, MMPI, MMP9, MS4A1, MUC1, MUC17, MUC2, Ncam, NGAL,NNMT, OPN, p53, PCSA, PDGFRB, PRL, PSMA, PSME3, Reg IV, SCRN1, Sept-9,SPARC, SPON2, SPR, SRVN, TFF3, TGM2, TIMP-1, TMEM211, TNF-alpha, TPA,TPS, Trail-R2, Trail-R4, TrKB, TROP2, Tsg 101, TWEAK, UNC93A, VEGFAColorectal cancer miR 92, miR 21, miR 9, miR 491 Colorectal cancermiR-127-3p, miR-92a, miR-486-3p, miR-378 Colorectal cancer TMEM211,MUC1, CD24 and/or GPR110 (GPCR 110) Colorectal cancer hsa-miR-376c,hsa-miR-215, hsa-miR-652, hsa-miR-582-5p, hsa-miR-324-5p, hsa-miR-1296,hsa-miR-28-5p, hsa-miR-190, hsa-miR-590-5p, hsa-miR-202, hsa- miR-195Colorectal cancer A26C1A, A26C1B, A2M, ACAA2, ACE, ACOT7, ACP1, ACTA1,ACTA2, vesicle markers ACTB, ACTBL2, ACTBL3, ACTC1, ACTG1, ACTG2, ACTN1,ACTN2, ACTN4, ACTR3, ADAM10, ADSL, AGR2, AGR3, AGRN, AHCY, AHNAK,AKR1B10, ALB, ALDH16A1, ALDH1A1, ALDOA, ANXA1, ANXA11, ANXA2, ANXA2P2,ANXA4, ANXA5, ANXA6, AP2A1, AP2A2, APOA1, ARF1, ARF3, ARF4, ARF5, ARF6,ARHGDIA, ARPC3, ARPC5L, ARRDC1, ARVCF, ASCC3L1, ASNS, ATP1A1, ATP1A2,ATP1A3, ATP1B1, ATP4A, ATP5A1, ATP5B, ATP5I, ATP5L, ATP5O, ATP6AP2, B2M,BAIAP2, BAIAP2L1, BRI3BP, BSG, BUB3, C1orf58, C5orf32, CAD, CALM1,CALM2, CALM3, CAND1, CANX, CAPZA1, CBR1, CBR3, CCT2, CCT3, CCT4, CCT5,CCT6A, CCT7, CCT8, CD44, CD46, CD55, CD59, CD63, CD81, CD82, CD9, CDC42,CDH1, CDH17, CEACAM5, CFL1, CFL2, CHMP1A, CHMP2A, CHMP4B, CKB, CLDN3,CLDN4, CLDN7, CLIC1, CLIC4, CLSTN1, CLTC, CLTCL1, CLU, COL12A1, COPB1,COPB2, CORO1C, COX4I1, COX5B, CRYZ, CSPG4, CSRP1, CST3, CTNNA1, CTNNB1,CTNND1, CTTN, CYFIP1, DCD, DERA, DIP2A, DIP2B, DIP2C, DMBT1, DPEP1,DPP4, DYNC1H1, EDIL3, EEF1A1, EEF1A2, EEF1AL3, EEF1G, EEF2, EFNB1, EGFR,EHD1, EHD4, EIF3EIP, EIF3I, EIF4A1, EIF4A2, ENO1, ENO2, ENO3, EPHA2,EPHA5, EPHB1, EPHB2, EPHB3, EPHB4, EPPK1, ESD, EZR, F11R, F5, F7,FAM125A, FAM125B, FAM129B, FASLG, FASN, FAT, FCGBP, FER1L3, FKBP1A,FLNA, FLNB, FLOT1, FLOT2, G6PD, GAPDH, GARS, GCN1L1, GDI2, GK, GMDS,GNA13, GNAI2, GNAI3, GNAS, GNB1, GNB2, GNB2L1, GNB3, GNB4, GNG12,GOLGA7, GPA33, GPI, GPRC5A, GSN, GSTP1, H2AFJ, HADHA, hCG_1757335, HEPH,HIST1H2AB, HIST1H2AE, HIST1H2AJ, HIST1H2AK, HIST1H4A, HIST1H4B,HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J,HIST1H4K, HIST1H4L, HIST2H2AC, HIST2H4A, HIST2H4B, HIST3H2A, HIST4H4,HLA- A, HLA-A29.1, HLA-B, HLA-C, HLA-E, HLA-H, HNRNPA2B1, HNRNPH2,HPCAL1, HRAS, HSD17B4, HSP90AA1, HSP90AA2, HSP90AA4P, HSP90AB1,HSP90AB2P, HSP90AB3P, HSP90B1, HSPA1A, HSPA1B, HSPA1L, HSPA2, HSPA4,HSPA5, HSPA6, HSPA7, HSPA8, HSPA9, HSPD1, HSPE1, HSPG2, HYOU1, IDH1,IFITM1, IFITM2, IFITM3, IGH@, IGHG1, IGHG2, IGHG3, IGHG4, IGHM,IGHV4-31, IGK@, IGKC, IGKV1-5, IGKV2- 24, IGKV3-20, IGSF3, IGSF8,IQGAP1, IQGAP2, ITGA2, ITGA3, ITGA6, ITGAV, ITGB1, ITGB4, JUP, KIAA0174,KIAA1199, KPNB1, KRAS, KRT1, KRT10, KRT13, KRT14, KRT15, KRT16, KRT17,KRT18, KRT19, KRT2, KRT20, KRT24, KRT25, KRT27, KRT28, KRT3, KRT4, KRT5,KRT6A, KRT6B, KRT6C, KRT7, KRT75, KRT76, KRT77, KRT79, KRT8, KRT9,LAMA5, LAMP1, LDHA, LDHB, LFNG, LGALS3, LGALS3BP, LGALS4, LIMA1, LIN7A,LIN7C, LOC100128936, LOC100130553, LOC100133382, LOC100133739,LOC284889, LOC388524, LOC388720, LOC442497, LOC653269, LRP4, LRPPRC,LRSAM1, LSR, LYZ, MAN1A1, MAP4K4, MARCKS, MARCKSL1, METRNL, MFGE8, MICA,MIF, MINK1, MITD1, MMP7, MOBKL1A, MSN, MTCH2, MUC13, MYADM, MYH10,MYH11, MYH14, MYH9, MYL6, MYL6B, MYO1C, MYO1D, NARS, NCALD, NCSTN,NEDD4, NEDD4L, NME1, NME2, NOTCH1, NQO1, NRAS, P4HB, PCBP1, PCNA, PCSK9,PDCD6, PDCD6IP, PDIA3, PDXK, PEBP1, PFN1, PGK1, PHB, PHB2, PKM2, PLEC1,PLEKHB2, PLSCR3, PLXNA1, PLXNB2, PPIA, PPIB, PPP2R1A, PRDX1, PRDX2,PRDX3, PRDX5, PRDX6, PRKAR2A, PRKDC, PRSS23, PSMA2, PSMC6, PSMD11,PSMD3, PSME3, PTGFRN, PTPRF, PYGB, QPCT, QSOX1, RAB10, RAB11A, RAB11B,RAB13, RAB14, RAB15, RAB1A, RAB1B, RAB2A, RAB33B, RAB35, RAB43, RAB4B,RAB5A, RAB5B, RAB5C, RAB6A, RAB6B, RAB7A, RAB8A, RAB8B, RAC1, RAC3,RALA, RALB, RAN, RANP1, RAP1A, RAP1B, RAP2A, RAP2B, RAP2C, RDX, REG4,RHOA, RHOC, RHOG, ROCK2, RP11-631M21.2, RPL10A, RPL12, RPL6, RPL8,RPLP0, RPLP0-like, RPLP 1, RPLP2, RPN1, RPS13, RPS14, RPS15A, RPS16,RPS18, RPS20, RPS21, RPS27A, RPS3, RPS4X, RPS4Y1, RPS4Y2, RPS7, RPS8,RPSA, RPSAP15, RRAS, RRAS2, RUVBL1, RUVBL2, S100A10, S100A11, S100A14,S100A16, S100A6, S100P, SDC1, SDC4, SDCBP, SDCBP2, SERINC1, SERINC5,SERPINA1, SERPINF1, SETD4, SFN, SLC12A2, SLC12A7, SLC16A1, SLC1A5,SLC25A4, SLC25A5, SLC25A6, SLC29A1, SLC2A1, SLC3A2, SLC44A1, SLC7A5,SLC9A3R1, SMPDL3B, SNAP23, SND1, SOD1, SORT1, SPTAN1, SPTBN1, SSBP1,SSR4, TACSTD1, TAGLN2, TBCA, TCEB1, TCP1, TF, TFRC, THBS1, TJP2, TKT,TMED2, TNFSF10, TNIK, TNKS1BP1, TNPO3, TOLLIP, TOMM22, TPI1, TPM1,TRAP1, TSG101, TSPAN1, TSPAN14, TSPAN15, TSPAN6, TSPAN8, TSTA3, TTYH3,TUBA1A, TUBA1B, TUBA1C, TUBA3C, TUBA3D, TUBA3E, TUBA4A, TUBA4B, TUBA8,TUBB, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4, TUBB4Q, TUBB6, TUFM, TXN,UBA1, UBA52, UBB, UBC, UBE2N, UBE2V2, UGDH, UQCRC2, VAMP1, VAMP3, VAMP8,VCP, VIL1, VPS25, VPS28, VPS35, VPS36, VPS37B, VPS37C, WDR1, YWHAB,YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ Colorectal Cancer hsa-miR-16,hsa-miR-25, hsa-miR-125b, hsa-miR-451, hsa-miR-200c, hsa-miR- 140-3p,hsa-miR-658, hsa-miR-370, hsa-miR-1296, hsa-miR-636, hsa-miR-502- 5pProstate Cancer NY-ESO-1, SSX-2, SSX-4, XAGE-1b, AMACR, p90 autoantigen,LEDGF Breast cancer miR-21, miR-155, miR-206, miR-122a, miR-210, miR-21,miR-155, miR-206, miR-122a, miR-210, let-7, miR-10b, miR-125a, miR-125b,miR-145, miR-143, miR-145, miR-1b Breast cancer GAS5 Breast cancer ER,PR, HER2, MUC1, EGFR, KRAS, B-Raf, CYP2D6, hsp70, MART-1, TRP, HER2,hsp70, MART-1, TRP, HER2, ER, PR, Class III b-tubulin, VEGFA,ETV6-NTRK3, BCA-225, hsp70, MART1, ER, VEGFA, Class III b-tubulin,HER2/neu (e.g., for Her2+ breast cancer), GPR30, ErbB4 (JM) isoform,MPR8, MISIIR, CD9, EphA2, EGFR, B7H3, PSM, PCSA, CD63, STEAP, CD81,ICAM1, A33, DR3, CD66e, MFG-E8, TROP-2, Mammaglobin, Hepsin, NPGP/NPFF2,PSCA, 5T4, NGAL, EpCam, neurokinin receptor-1 (NK-1 or NK- 1R), NK-2,Pai-1, CD45, CD10, HER2/ERBB2, AGTR1, NPY1R, MUC1, ESA, CD133, GPR30,BCA225, CD24, CA15.3 (MUC1 secreted), CA27.29 (MUC1 secreted), NMDAR1,NMDAR2, MAGEA, CTAG1B, NY-ESO-1, SPB, SPC, NSE, PGP9.5, progesteronereceptor (PR) or its isoform (PR(A) or PR(B)), P2RX7, NDUFB7, NSE, GAL3,osteopontin, CHI3L1, IC3b, mesothelin, SPA, AQP5, GPCR, hCEA-CAM, PTPIA-2, CABYR, TMEM211, ADAM28, UNC93A, MUC17, MUC2, IL10R-beta, BCMA,HVEM/TNFRSF14, Trappin-2, Elafin, ST2/IL1 R4, TNFRF14, CEACAM1, TPA1,LAMP, WF, WH1000, PECAM, BSA, TNFR Breast cancer CD9, MIS Rii, ER, CD63,MUC1, HER3, STAT3, VEGFA, BCA, CA125, CD24, EPCAM, ERB B4 Breast cancerCD10, NPGP/NPFF2, HER2/ERBB2, AGTR1, NPY1R, neurokinin receptor-1 (NK-1or NK-1R), NK-2, MUC1, ESA, CD133, GPR30, BCA225, CD24, CA15.3 (MUC1secreted), CA27.29 (MUC1 secreted), NMDAR1, NMDAR2, MAGEA, CTAG1B,NY-ESO-1 Breast cancer SPB, SPC, NSE, PGP9.5, CD9, P2RX7, NDUFB7, NSE,GAL3, osteopontin, CHI3L1, EGFR, B7H3, IC3b, MUC1, mesothelin, SPA,PCSA, CD63, STEAP, AQP5, CD81, DR3, PSM, GPCR, EphA2, hCEA-CAM, PTPIA-2, CABYR, TMEM211, ADAM28, UNC93A, A33, CD24, CD10, NGAL, EpCam,MUC17, TROP-2, MUC2, IL10R-beta, BCMA, HVEM/TNFRSF14, Trappin-2 Elafin,ST2/IL1 R4, TNFRF14, CEACAM1, TPA1, LAMP, WF, WH1000, PECAM, BSA, TNFRBreast cancer BRCA, MUC-1, MUC 16, CD24, ErbB4, ErbB2 (HER2), ErbB3,HSP70, Mammaglobin, PR, PR(B), VEGFA Breast cancer CD9, HSP70, Gal3,MIS, EGFR, ER, ICB3, CD63, B7H4, MUC1, DLL4, CD81, ERB3, VEGF, BCA225,BRCA, CA125, CD174, CD24, ERB2, NGAL, GPR30, CYFRA21, CD31, cMET, MUC2,ERBB4 Breast cancer CD9, EphA2, EGFR, B7H3, PSMA, PCSA, CD63, STEAP,CD81, STEAP1, ICAM1 (CD54), PSMA, A33, DR3, CD66e, MFG-8e, TMEM211,TROP-2, EGFR, Mammoglobin, Hepsin, NPGP/NPFF2, PSCA, 5T4, NGAL, NK-2,EpCam, NK-1R, PSMA, 5T4, PAI-1, CD45 Breast cancer PGP9.5, CD9, HSP70,gal3-b2c10, EGFR, iC3b, PSMA, PCSA, CD63, MUC1, DLL4, CD81, B7-H3, HER 3(ErbB3), MART-1, PSA, VEGF A, TIMP-1, GPCR GPR110, EphA2, MMP9, mmp7,TMEM211, UNC93a, BRCA, CA125 (MUC16), Mammaglobin, CD174 (Lewis y),CD66e CEA, CD24 c.sn3, C-erbB2, CD10, NGAL, epcam, CEA (carcinoembryonicAntigen), GPR30, CYFRA21-1, OPN, MUC17, hVEGFR2, MUC2, NCAM, ASPH,ErbB4, SPB, SPC, CD9, MS4A1, EphA2, MIS RII, HER2 (ErbB2), ER, PR (B),MRP8, CD63, B7H4, TGM2, CD81, DR3, STAT 3, MACC-1, TrKB, IL 6 Unc,OPG-13, IL6R, EZH2, SCRN1, TWEAK, SERPINB3, CDAC1, BCA-225, DR3, A33,NPGP/NPFF2, TIMP1, BDNF, FRT, Ferritin heavy chain, seprase, p53, LDH,HSP, ost, p53, CXCL12, HAP, CRP, Gro-alpha, Tsg 101, GDF15 Breast cancerCD9, HSP70, Gal3, MIS (RII), EGFR, ER, ICB3, CD63, B7H4, MUC1, CD81,ERB3, MART1, STAT3, VEGF, BCA225, BRCA, CA125, CD174, CD24, ERB2, NGAL,GPR30, CYFRA21, CD31, cMET, MUC2, ERB4, TMEM211 Breast Cancer 5T4(trophoblast), ADAM10, AGER/RAGE, APC, APP (β-amyloid), ASPH (A- 10),B7H3 (CD276), BACE1, BAI3, BRCA1, BDNF, BIRC2, C1GALT1, CA125 (MUC16),Calmodulin 1, CCL2 (MCP-1), CD9, CD10, CD127 (IL7R), CD174, CD24, CD44,CD63, CD81, CEA, CRMP-2, CXCR3, CXCR4, CXCR6, CYFRA 21, derlin 1, DLL4,DPP6, E-CAD, EpCaM, EphA2 (H-77), ER(1) ESR1α, ER(2) ESR2β, Erb B4,Erbb2, erb3 (Erb-B3), PA2G4, FRT (FLT1), Gal3, GPR30 (G- coupled ER1),HAP1, HER3, HSP-27, HSP70, IC3b, IL8, insig, junction plakoglobin,Keratin 15, KRAS, Mammaglobin, MART1, MCT2, MFGE8, MMP9, MRP8, Muc1,MUC17, MUC2, NCAM, NG2 (CSPG4), Ngal, NHE-3, NT5E (CD73), ODC1, OPG,OPN, p53, PARK7, PCSA, PGP9.5 (PARK5), PR(B), PSA, PSMA, RAGE, STXBP4,Survivin, TFF3 (secreted), TIMP1, TIMP2, TMEM211, TRAF4 (scaffolding),TRAIL-R2 (death Receptor 5), TrkB, Tsg 101, UNC93a, VEGF A, VEGFR2,YB-1, VEGFR1, GCDPF-15 (PIP), BigH3 (TGFb1-induced protein), 5HT2B(serotonin receptor 2B), BRCA2, BACE1, CDH1-cadherin Breast CancerAK5.2, ATP6V1B1, CRABP1 Breast Cancer DST.3, GATA3, KRT81 Breast CancerAK5.2, ATP6V1B1, CRABP1, DST.3, ELF5, GATA3, KRT81, LALBA, OXTR,RASL10A, SERHL, TFAP2A.1, TFAP2A.3, TFAP2C, VTCN1 Breast Cancer TRAP;Renal Cell Carcinoma; Filamin; 14.3.3, Pan; Prohibitin; c-fos; Ang-2;GSTmu; Ang-1; FHIT; Rad51; Inhibin alpha; Cadherin-P; 14.3.3 gamma;p18INK4c; P504S; XRCC2; Caspase 5; CREB-Binding Protein; EstrogenReceptor; IL17; Claudin 2; Keratin 8; GAPDH; CD1; Keratin, LMW; GammaGlutamylcysteine Synthetase(GCS)/Glutamate-cysteine Ligase;a-B-Crystallin; Pax-5; MMP-19; APC; IL-3; Keratin 8 (phospho-specificSer73); TGF-beta 2; ITK; Oct-2/; DJ-1; B7-H2; Plasma Cell Marker; Rad18;Estriol; Chk1; Prolactin Receptor; Laminin Receptor; Histone H1; CD45RO;GnRH Receptor; IP10/CRG2; Actin, Muscle Specific; S100; Dystrophin;Tubulin-a; CD3zeta; CDC37; GABA a Receptor 1; MMP-7 (Matrilysin);Heregulin; Caspase 3; CD56/NCAM-1; Gastrin 1; SREBP-1 (Sterol RegulatoryElement Binding Protein-1); MLH1; PGP9.5; Factor VIII Related Antigen;ADP-ribosylation Factor (ARF-6); MHC II (HLA-DR) Ia; Survivin; CD23;G-CSF; CD2; Calretinin; Neuron Specific Enolase; CD165; Calponin;CD95/Fas; Urocortin; Heat Shock Protein 27/hsp27; Topo II beta; InsulinReceptor; Keratin 5/8; sm; Actin, skeletal muscle; CA19-9; GluR1; GRIP1;CD79a mb-1; TdT; HRP; CD94; CCK-8; Thymidine Phosphorylase; CD57;Alkaline Phosphatase (AP); CD59/MACIF/ MIRL/Protectin; GLUT-1;alpha-1-antitrypsin; Presenillin; Mucin 3 (MUC3); pS2; 14-3-3 beta;MMP-13 (Collagenase-3); Fli-1; mGluR5; Mast Cell Chymase; Laminin B1/b1;Neurofilament (160 kDa); CNPase; Amylin Peptide; Gai1; CD6;alpha-1-antichymotrypsin; E2F-2; MyoD1 Ductal carcinoma in LamininB1/b1; E2F-2; TdT; Apolipoprotein D; Granulocyte; Alkaline situ (DCIS)Phosphatase (AP); Heat Shock Protein 27/hsp27; CD95/Fas; pS2; Estriol;GLUT-1; Fibronectin; CD6; CCK-8; sm; Factor VIII Related Antigen; CD57;Plasminogen; CD71/Transferrin Receptor; Keratin 5/8; ThymidinePhosphorylase; CD45/T200/LCA; Epithelial Specific Antigen; Macrophage;CD10; MyoD1; Gai1; bcl-XL; hPL; Caspase 3; Actin, skeletal muscle;IP10/CRG2; GnRH Receptor; p35nck5a; ADP-ribosylation Factor (ARF-6);Cdk4; alpha-1-antitrypsin; IL17; Neuron Specific Enolase; CD56/NCAM-1;Prolactin Receptor; Cdk7; CD79a mb-1; Collagen IV; CD94; MyeloidSpecific Marker; Keratin 10; Pax-5; IgM (m-Heavy Chain); CD45RO; CA19-9;Mucin 2; Glucagon; Mast Cell Chymase; MLH1; CD1; CNPase; Parkin; MHC II(HLA- DR) Ia; B7-H2; Chk1; Lambda Light Chain; MHC II (HLA-DP and DR);Myogenin; MMP-7 (Matrilysin); Topo II beta; CD53; Keratin 19; Rad18; RetOncoprotein; MHC II (HLA-DP); E3-binding protein (ARM1); ProgesteroneReceptor; Keratin 8; IgG; IgA; Tubulin; Insulin Receptor Substrate-1;Keratin 15; DR3; IL-3; Keratin 10/13; Cyclin D3; MHC I (HLA25 andHLA-Aw32); Calmodulin; Neurofilament (160 kDa) Ductal carcinoma inMacrophage; Fibronectin; Granulocyte; Keratin 19; Cyclin D3;CD45/T200/LCA; situ (DCIS) v. other EGFR; Thrombospondin; CD81/TAPA-1;Ruv C; Plasminogen; Collagen IV; Breast cancer Laminin B1/b1; CD10; TdT;Filamin; bcl-XL; 14.3.3 gamma; 14.3.3, Pan; p170; Apolipoprotein D;CD71/Transferrin Receptor; FHIT Lung cancer Pgrmc1 (progesteronereceptor membrane component 1)/sigma-2 receptor, STEAP, EZH2 Lung cancerProhibitin, CD23, Amylin Peptide, HRP, Rad51, Pax-5, Oct-3/, GLUT-1,PSCA, Thrombospondin, FHIT, a-B-Crystallin, LewisA, Vacular EndothelialGrowth Factor(VEGF), Hepatocyte Factor Homologue-4, Flt-4, GluR6/7,Prostate Apoptosis Response Protein-4, GluR1, Fli-1, Urocortin, S100A4,14-3-3 beta, P504S, HDAC1, PGP9.5, DJ-1, COX2, MMP-19, Actin, skeletalmuscle, Claudin 3, Cadherin-P, Collagen IX, p27Kip1, Cathepsin D, CD30(Reed-Sternberg Cell Marker), Ubiquitin, FSH-b, TrxR2, CCK-8, Cyclin C,CD138, TGF-beta 2, Adrenocorticotrophic Hormone, PPAR-gamma, Bcl-6,GLUT-3, IGF-I, mRANKL, Fas-ligand, Filamin, Calretinin, O ct-1,Parathyroid Hormone, Claudin 5, Claudin 4, Raf-1 (Phospho-specific),CDC14A Phosphatase, Mitochondria, APC, Gastrin 1, Ku (p80), Gai1, XPA,Maltose Binding Protein, Melanoma (gp100), Phosphotyrosine, Amyloid A,CXCR4/Fusin, Hepatic Nuclear Factor- 3B, Caspase 1, HPV 16-E7, AxonalGrowth Cones, Lck, Ornithine Decarboxylase, Gamma GlutamylcysteineSynthetase(GCS)/Glutamate-cysteine Ligase, ERCC1, Calmodulin, Caspase 7(Mch 3), CD137 (4-1BB), Nitric Oxide Synthase, brain (bNOS), E2F-2,IL-10R, L-Plastin, CD18, Vimentin, CD50/ICAM-3, Superoxide Dismutase,Adenovirus Type 5 E1A, PHAS-I, Progesterone Receptor(phospho-specific) - Serine 294, MHC II (HLA-DQ), XPG, ER Ca+2 ATPase2,Laminin-s, E3-binding protein (ARM1), CD45RO, CD1, Cdk2, MMP-10(Stromilysin-2), sm, Surfactant Protein B (Pro), Apolipoprotein D, CD46,Keratin 8 (phospho-specific Ser73), PCNA, PLAP, CD20, Syk, LH, Keratin19, ADP-ribosylation Factor (ARF-6), Int-2 Oncoprotein, Luciferase, AIF(Apoptosis Inducing Factor), Grb2, bcl-X, CD16, Paxillin, MHC II (HLA-DPand DR), B-Cell, p21WAF1, MHC II (HLA-DR), Tyrosinase, E2F-1, Pds1,Calponin, Notch, CD26/DPP IV, SV40 Large T Antigen, Ku (p70/p80),Perforin, XPF, SIM Ag (SIMA-4D3), Cdk1/p34cdc2, Neuron Specific Enolase,b-2-Microglobulin, DNA Polymerase Beta, Thyroid Hormone Receptor, Human,Alkaline Phosphatase (AP), Plasma Cell Marker, Heat Shock Protein70/hsp70, TRP75/ gp75, SRF (Serum Response Factor), Laminin B1/b1, MastCell Chymase, Caldesmon, CEA/CD66e, CD24, Retinoid X Receptor (hRXR),CD45/T200/LCA, Rabies Virus, Cytochrome c, DR3, bcl-XL, Fascin, CD71/Transferrin Receptor Lung Cancer miR-497 Ovarian Cancer CA-125, CA 19-9,c-reactive protein, CD95(also called Fas, Fas antigen, Fas receptor,FasR, TNFRSF6, APT1 or APO-1), FAP-1, miR-200 microRNAs, EGFR, EGFRvIII,apolipoprotein AI, apolipoprotein CIII, myoglobin, tenascin C, MSH6,claudin-3, claudin-4, caveolin-1, coagulation factor III, CD9, CD36,CD37, CD53, CD63, CD81, CD136, CD147, Hsp70, Hsp90, Rab13, Desmocollin-1, EMP-2, CK7, CK20, GCDF15, CD82, Rab-5b, Annexin V, MFG-E8 and HLA-DR. MiR-200 microRNAs (miR-200a, miR-200b, miR-200c), miR-141, miR-429,JNK, Jun Prostate Cancer v AQP2, BMP5, C16orf86, CXCL13, DST, ERCC1,GNAO1, KLHL5, MAP4K1, normal NELL2, PENK, PGF, POU3F1, PRSS21, SCML1,SEMG1, SMARCD3, SNAI2, TAF1C, TNNT3 Prostate Cancer v ADRB2, ARG2,C22orf32, CYorf14, EIF1AY, FEV, KLK2, KLK4, LRRC26, Breast Cancer MAOA,NLGN4Y, PNPLA7, PVRL3, SIM2, SLC30A4, SLC45A3, STX19, TRIM36, TRPM8Prostate Cancer v ADRB2, BAIAP2L2, C19orf33, CDX1, CEACAM6, EEF1A2,ERN2, FAM110B, Colorectal Cancer FOXA2, KLK2, KLK4, LOC389816, LRRC26,MIPOL1, SLC45A3, SPDEF, TRIM31, TRIM36, ZNF613 Prostate Cancer v ASTN2,CAB39L, CRIP1, FAM110B, FEV, GSTP1, KLK2, KLK4, LOC389816, Lung CancerLRRC26, MUC1, PNPLA7, SIM2, SLC45A3, SPDEF, TRIM36, TRPV6, ZNF613Prostate Cancer miRs-26a+b, miR-15, miR-16, miR-195, miR-497, miR-424,miR-206, miR-342- 5p, miR-186, miR-1271, miR-600, miR-216b, miR-519family, miR-203 Integrins ITGA1 (CD49a, VLA1), ITGA2 (CD49b, VLA2),ITGA3 (CD49c, VLA3), ITGA4 (CD49d, VLA4), ITGA5 (CD49e, VLA5), ITGA6(CD49f, VLA6), ITGA7 (FLJ25220), ITGA8, ITGA9 (RLC), ITGA10, ITGA11(HsT18964), ITGAD (CD11D, FLJ39841), ITGAE (CD103, HUMINAE), ITGAL(CD11a, LFA1A), ITGAM (CD11b, MAC-1), ITGAV (CD51, VNRA, MSK8), ITGAW,ITGAX (CD11c), ITGB1 (CD29, FNRB, MSK12, MDF20), ITGB2 (CD18, LFA- 1,MAC-1, MFI7), ITGB3 (CD61, GP3A, GPIIIa), ITGB4 (CD104), ITGB5(FLJ26658), ITGB6, ITGB7, ITGB8 Glycoprotein GpIa-IIa, GpIIb-IIIa,GpIIIb, GpIb, GpIX Transcription factors STAT3, EZH2, p53, MACC1, SPDEF,RUNX2, YB-1 Kinases AURKA, AURKB Disease Markers 6Ckine, Adiponectin,Adrenocorticotropic Hormone, Agouti-Related Protein, Aldose Reductase,Alpha-1-Antichymotrypsin, Alpha-1-Antitrypsin, Alpha-1- Microglobulin,Alpha-2-Macroglobulin, Alpha-Fetoprotein, Amphiregulin, Angiogenin,Angiopoietin-2, Angiotensin-Converting Enzyme, Angiotensinogen, AnnexinA1, Apolipoprotein A-I, Apolipoprotein A-II, Apolipoprotein A-IV,Apolipoprotein B, Apolipoprotein C-I, Apolipoprotein C-III,Apolipoprotein D, Apolipoprotein E, Apolipoprotein H, Apolipoprotein(a),AXL Receptor Tyrosine Kinase, B cell-activating Factor, B LymphocyteChemoattractant, Bcl-2-like protein 2, Beta-2-Microglobulin,Betacellulin, Bone Morphogenetic Protein 6, Brain-Derived NeurotrophicFactor, Calbindin, Calcitonin, Cancer Antigen 125, Cancer Antigen 15-3,Cancer Antigen 19-9, Cancer Antigen 72-4, Carcinoembryonic Antigen,Cathepsin D, CD 40 antigen, CD40 Ligand, CD5 Antigen-like, CellularFibronectin, Chemokine CC-4, Chromogranin-A, Ciliary NeurotrophicFactor, Clusterin, Collagen IV, Complement C3, Complement Factor H,Connective Tissue Growth Factor, Cortisol, C-Peptide, C-ReactiveProtein, Creatine Kinase-MB, Cystatin-C, Endoglin, Endostatin,Endothelin-1, EN-RAGE, Eotaxin-1, Eotaxin-2, Eotaxin-3, Epidermal GrowthFactor, Epiregulin, Epithelial cell adhesion molecule,Epithelial-Derived Neutrophil- Activating Protein 78, Erythropoietin,E-Selectin, Ezrin, Factor VII, Fas Ligand, FASLG Receptor, FattyAcid-Binding Protein (adipocyte), Fatty Acid-Binding Protein (heart),Fatty Acid-Binding Protein (liver), Ferritin, Fetuin-A, Fibrinogen,Fibroblast Growth Factor 4, Fibroblast Growth Factor basic, Fibulin-1C,Follicle- Stimulating Hormone, Galectin-3, Gelsolin, Glucagon,Glucagon-like Peptide 1, Glucose-6-phosphate Isomerase,Glutamate-Cysteine Ligase Regulatory subunit, Glutathione S-Transferasealpha, Glutathione S-Transferase Mu 1, Granulocyte Colony-StimulatingFactor, Granulocyte-Macrophage Colony-Stimulating Factor, GrowthHormone, Growth-Regulated alpha protein, Haptoglobin, HE4, Heat ShockProtein 60, Heparin-Binding EGF-Like Growth Factor, Hepatocyte GrowthFactor, Hepatocyte Growth Factor Receptor, Hepsin, Human ChorionicGonadotropin beta, Human Epidermal Growth Factor Receptor 2,Immunoglobulin A, Immunoglobulin E, Immunoglobulin M, Insulin,Insulin-like Growth Factor I, Insulin-like Growth Factor-Binding Protein1, Insulin-like Growth Factor-Binding Protein 2, Insulin-like GrowthFactor-Binding Protein 3, Insulin-like Growth Factor Binding Protein 4,Insulin-like Growth Factor Binding Protein 5, Insulin-like Growth FactorBinding Protein 6, Intercellular Adhesion Molecule 1, Interferon gamma,Interferon gamma Induced Protein 10, Interferon- inducible T-cell alphachemoattractant, Interleukin-1 alpha, Interleukin-1 beta, Interleukin-1Receptor antagonist, Interleukin-2, Interleukin-2 Receptor alpha,Interleukin-3, Interleukin-4, Interleukin-5, Interleukin-6,Interleukin-6 Receptor, Interleukin-6 Receptor subunit beta,Interleukin-7, Interleukin-8, Interleukin-10, Interleukin-11,Interleukin-12 Subunit p40, Interleukin-12 Subunit p70, Interleukin-13,Interleukin-15, Interleukin-16, Interleukin-25, Kallikrein 5,Kallikrein-7, Kidney Injury Molecule-1, Lactoylglutathione lyase,Latency- Associated Peptide of Transforming Growth Factor beta 1,Lectin-Like Oxidized LDL Receptor 1, Leptin, Luteinizing Hormone,Lymphotactin, Macrophage Colony-Stimulating Factor 1, MacrophageInflammatory Protein-1 alpha, Macrophage Inflammatory Protein-1 beta,Macrophage Inflammatory Protein-3 alpha, Macrophage inflammatory protein3 beta, Macrophage Migration Inhibitory Factor, Macrophage-DerivedChemokine, Macrophage-Stimulating Protein, Malondialdehyde-ModifiedLow-Density Lipoprotein, Maspin, Matrix Metalloproteinase-1, MatrixMetalloproteinase-2, Matrix Metalloproteinase-3, MatrixMetalloproteinase-7, Matrix Metalloproteinase-9, MatrixMetalloproteinase-9, Matrix Metalloproteinase-10, Mesothelin, MHC classI chain-related protein A, Monocyte Chemotactic Protein 1, MonocyteChemotactic Protein 2, Monocyte Chemotactic Protein 3, MonocyteChemotactic Protein 4, Monokine Induced by Gamma Interferon, MyeloidProgenitor Inhibitory Factor 1, Myeloperoxidase, Myoglobin, Nerve GrowthFactor beta, Neuronal Cell Adhesion Molecule, Neuron-Specific Enolase,Neuropilin-1, Neutrophil Gelatinase- Associated Lipocalin, NT-proBNP,Nucleoside diphosphate kinase B, Osteopontin, Osteoprotegerin,Pancreatic Polypeptide, Pepsinogen I, Peptide YY, Peroxiredoxin-4,Phosphoserine Aminotransferase, Placenta Growth Factor, PlasminogenActivator Inhibitor 1, Platelet-Derived Growth Factor BB,Pregnancy-Associated Plasma Protein A, Progesterone, Proinsulin (inc.Total or Intact), Prolactin, Prostasin, Prostate-Specific Antigen (inc.Free PSA), Prostatic Acid Phosphatase, Protein S100-A4, Protein S100-A6,Pulmonary and Activation- Regulated Chemokine, Receptor for advancedglycosylation end products, Receptor tyrosine-protein kinase erbB-3,Resistin, S100 calcium-binding protein B, Secretin, Serotransferrin,Serum Amyloid P-Component, Serum Glutamic Oxaloacetic Transaminase, SexHormone-Binding Globulin, Sortilin, Squamous Cell Carcinoma Antigen-1,Stem Cell Factor, Stromal cell-derived Factor-1, Superoxide Dismutase 1(soluble), T Lymphocyte-Secreted Protein I-309, Tamm- Horsfall UrinaryGlycoprotein, T-Cell-Specific Protein RANTES, Tenascin-C, Testosterone,Tetranectin, Thrombomodulin, Thrombopoietin, Thrombospondin-1,Thyroglobulin, Thyroid-Stimulating Hormone, Thyroxine-Binding Globulin,Tissue Factor, Tissue Inhibitor of Metalloproteinases 1, Tissue typePlasminogen activator, TNF-Related Apoptosis-Inducing Ligand Receptor 3,Transforming Growth Factor alpha, Transforming Growth Factor beta-3,Transthyretin, Trefoil Factor 3, Tumor Necrosis Factor alpha, TumorNecrosis Factor beta, Tumor Necrosis Factor Receptor I, Tumor necrosisFactor Receptor 2, Tyrosine kinase with Ig and EGF homology domains 2,Urokinase-type Plasminogen Activator, Urokinase-type plasminogenactivator Receptor, Vascular Cell Adhesion Molecule-1, VascularEndothelial Growth Factor, Vascular endothelial growth Factor B,Vascular Endothelial Growth Factor C, Vascular endothelial growth FactorD, Vascular Endothelial Growth Factor Receptor 1, Vascular EndothelialGrowth Factor Receptor 2, Vascular endothelial growth Factor Receptor 3,Vitamin K-Dependent Protein S, Vitronectin, von Willebrand Factor,YKL-40 Disease Markers Adiponectin, Adrenocorticotropic Hormone,Agouti-Related Protein, Alpha-1- Antichymotrypsin, Alpha-1-Antitrypsin,Alpha-1-Microglobulin, Alpha-2- Macroglobulin, Alpha-Fetoprotein,Amphiregulin, Angiopoietin-2, Angiotensin- Converting Enzyme,Angiotensinogen, Apolipoprotein A-I, Apolipoprotein A-II, ApolipoproteinA-IV, Apolipoprotein B, Apolipoprotein C-I, Apolipoprotein C- III,Apolipoprotein D, Apolipoprotein E, Apolipoprotein H, Apolipoprotein(a),AXL Receptor Tyrosine Kinase, B Lymphocyte Chemoattractant, Beta-2-Microglobulin, Betacellulin, Bone Morphogenetic Protein 6, Brain-DerivedNeurotrophic Factor, Calbindin, Calcitonin, Cancer Antigen 125, CancerAntigen 19-9, Carcinoembryonic Antigen, CD 40 antigen, CD40 Ligand, CD5Antigen- like, Chemokine CC-4, Chromogranin-A, Ciliary NeurotrophicFactor, Clusterin, Complement C3, Complement Factor H, Connective TissueGrowth Factor, Cortisol, C-Peptide, C-Reactive Protein, CreatineKinase-MB, Cystatin-C, Endothelin-1, EN-RAGE, Eotaxin-1, Eotaxin-3,Epidermal Growth Factor, Epiregulin, Epithelial-DerivedNeutrophil-Activating Protein 78, Erythropoietin, E-Selectin, FactorVII, Fas Ligand, FASLG Receptor, Fatty Acid-Binding Protein (heart),Ferritin, Fetuin-A, Fibrinogen, Fibroblast Growth Factor 4, FibroblastGrowth Factor basic, Follicle-Stimulating Hormone, Glucagon,Glucagon-like Peptide 1, Glutathione S-Transferase alpha, GranulocyteColony-Stimulating Factor, Granulocyte-Macrophage Colony-StimulatingFactor, Growth Hormone, Growth-Regulated alpha protein, Haptoglobin,Heat Shock Protein 60, Heparin- Binding EGF-Like Growth Factor,Hepatocyte Growth Factor, Immunoglobulin A, Immunoglobulin E,Immunoglobulin M, Insulin, Insulin-like Growth Factor I, Insulin-likeGrowth Factor-Binding Protein 2, Intercellular Adhesion Molecule 1,Interferon gamma, Interferon gamma Induced Protein 10, Interleukin-1alpha, Interleukin-1 beta, Interleukin-1 Receptor antagonist,Interleukin-2, Interleukin-3, Interleukin-4, Interleukin-5,Interleukin-6, Interleukin-6 Receptor, Interleukin-7, Interleukin-8,Interleukin-10, Interleukin-11, Interleukin-12 Subunit p40,Interleukin-12 Subunit p70, Interleukin-13, Interleukin-15,Interleukin-16, Interleukin-25, Kidney Injury Molecule-1, Lectin-LikeOxidized LDL Receptor 1, Leptin, Luteinizing Hormone, Lymphotactin,Macrophage Colony-Stimulating Factor 1, Macrophage InflammatoryProtein-1 alpha, Macrophage Inflammatory Protein-1 beta, MacrophageInflammatory Protein-3 alpha, Macrophage Migration Inhibitory Factor,Macrophage-Derived Chemokine, Malondialdehyde-Modified Low-DensityLipoprotein, Matrix Metalloproteinase-1, Matrix Metalloproteinase- 2,Matrix Metalloproteinase-3, Matrix Metalloproteinase-7, MatrixMetalloproteinase-9, Matrix Metalloproteinase-9, MatrixMetalloproteinase-10, Monocyte Chemotactic Protein 1, MonocyteChemotactic Protein 2, Monocyte Chemotactic Protein 3, MonocyteChemotactic Protein 4, Monokine Induced by Gamma Interferon, MyeloidProgenitor Inhibitory Factor 1, Myeloperoxidase, Myoglobin, Nerve GrowthFactor beta, Neuronal Cell Adhesion Molecule, NeutrophilGelatinase-Associated Lipocalin, NT-proBNP, Osteopontin, PancreaticPolypeptide, Peptide YY, Placenta Growth Factor, Plasminogen ActivatorInhibitor 1, Platelet-Derived Growth Factor BB, Pregnancy-AssociatedPlasma Protein A, Progesterone, Proinsulin (inc. Intact or Total),Prolactin, Prostate- Specific Antigen (inc. Free PSA), Prostatic AcidPhosphatase, Pulmonary and Activation-Regulated Chemokine, Receptor foradvanced glycosylation end products, Resistin, S100 calcium-bindingprotein B, Secretin, Serotransferrin, Serum Amyloid P-Component, SerumGlutamic Oxaloacetic Transaminase, Sex Hormone-Binding Globulin,Sortilin, Stem Cell Factor, Superoxide Dismutase 1 (soluble), TLymphocyte-Secreted Protein 1-309, Tamm-Horsfall Urinary Glycoprotein,T-Cell-Specific Protein RANTES, Tenascin-C, Testosterone,Thrombomodulin, Thrombopoietin, Thrombospondin-1, Thyroid-StimulatingHormone, Thyroxine-Binding Globulin, Tissue Factor, Tissue Inhibitor ofMetalloproteinases 1, TNF-Related Apoptosis-Inducing Ligand Receptor 3,Transforming Growth Factor alpha, Transforming Growth Factor beta-3,Transthyretin, Trefoil Factor 3, Tumor Necrosis Factor alpha, TumorNecrosis Factor beta, Tumor necrosis Factor Receptor 2, Vascular CellAdhesion Molecule- 1, Vascular Endothelial Growth Factor, VitaminK-Dependent Protein S, Vitronectin, von Willebrand Factor Oncology6Ckine, Aldose Reductase, Alpha-Fetoprotein, Amphiregulin, Angiogenin,Annexin A1, B cell-activating Factor, B Lymphocyte Chemoattractant,Bcl-2-like protein 2, Betacellulin, Cancer Antigen 125, Cancer Antigen15-3, Cancer Antigen 19-9, Cancer Antigen 72-4, CarcinoembryonicAntigen, Cathepsin D, Cellular Fibronectin, Collagen IV, Endoglin,Endostatin, Eotaxin-2, Epidermal Growth Factor, Epiregulin, Epithelialcell adhesion molecule, Ezrin, Fatty Acid-Binding Protein (adipocyte),Fatty Acid-Binding Protein (liver), Fibroblast Growth Factor basic,Fibulin-1C, Galectin-3, Gelsolin, Glucose-6-phosphate Isomerase,Glutamate-Cysteine Ligase Regulatory subunit, Glutathione S-TransferaseMu 1, HE4, Heparin-Binding EGF-Like Growth Factor, Hepatocyte GrowthFactor, Hepatocyte Growth Factor Receptor, Hepsin, Human ChorionicGonadotropin beta, Human Epidermal Growth Factor Receptor 2,Insulin-like Growth Factor- Binding Protein 1, Insulin-like GrowthFactor-Binding Protein 2, Insulin-like Growth Factor-Binding Protein 3,Insulin-like Growth Factor Binding Protein 4, Insulin-like Growth FactorBinding Protein 5, Insulin-like Growth Factor Binding Protein 6,Interferon gamma Induced Protein 10, Interferon-inducible T-cell alphachemoattractant, Interleukin-2 Receptor alpha, Interleukin-6,Interleukin-6 Receptor subunit beta, Kallikrein 5, Kallikrein-7,Lactoylglutathione lyase, Latency-Associated Peptide of TransformingGrowth Factor beta 1, Leptin, Macrophage inflammatory protein 3 beta,Macrophage Migration Inhibitory Factor, Macrophage-Stimulating Protein,Maspin, Matrix Metalloproteinase-2, Mesothelin, MHC class Ichain-related protein A, Monocyte Chemotactic Protein 1, MonokineInduced by Gamma Interferon, Neuron-Specific Enolase, Neuropilin- 1,Neutrophil Gelatinase-Associated Lipocalin, Nucleoside diphosphatekinase B, Osteopontin, Osteoprotegerin, Pepsinogen I, Peroxiredoxin-4,Phosphoserine Aminotransferase, Placenta Growth Factor, Platelet-DerivedGrowth Factor BB, Prostasin, Protein S100-A4, Protein S100-A6, Receptortyrosine-protein kinase erbB-3, Squamous Cell Carcinoma Antigen-1,Stromal cell-derived Factor-1, Tenascin-C, Tetranectin, Thyroglobulin,Tissue type Plasminogen activator, Transforming Growth Factor alpha,Tumor Necrosis Factor Receptor I, Tyrosine kinase with Ig and EGFhomology domains 2, Urokinase-type Plasminogen Activator, Urokinase-typeplasminogen activator Receptor, Vascular Endothelial Growth Factor,Vascular endothelial growth Factor B, Vascular Endothelial Growth FactorC, Vascular endothelial growth Factor D, Vascular Endothelial GrowthFactor Receptor 1, Vascular Endothelial Growth Factor Receptor 2,Vascular endothelial growth Factor Receptor 3, YKL-40 DiseaseAdiponectin, Alpha-1-Antitrypsin, Alpha-2-Macroglobulin,Alpha-Fetoprotein, Apolipoprotein A-I, Apolipoprotein C-III,Apolipoprotein H, Apolipoprotein(a), Beta-2-Microglobulin, Brain-DerivedNeurotrophic Factor, Calcitonin, Cancer Antigen 125, Cancer Antigen19-9, Carcinoembryonic Antigen, CD 40 antigen, CD40 Ligand, ComplementC3, C-Reactive Protein, Creatine Kinase-MB, Endothelin-1, EN-RAGE,Eotaxin-1, Epidermal Growth Factor, Epithelial- DerivedNeutrophil-Activating Protein 78, Erythropoietin, Factor VII, FattyAcid- Binding Protein (heart), Ferritin, Fibrinogen, Fibroblast GrowthFactor basic, Granulocyte Colony-Stimulating Factor,Granulocyte-Macrophage Colony- Stimulating Factor, Growth Hormone,Haptoglobin, Immunoglobulin A, Immunoglobulin E, Immunoglobulin M,Insulin, Insulin-like Growth Factor I, Intercellular Adhesion Molecule1, Interferon gamma, Interleukin-1 alpha, Interleukin-1 beta,Interleukin-1 Receptor antagonist, Interleukin-2, Interleukin-3,Interleukin-4, Interleukin-5, Interleukin-6, Interleukin-7,Interleukin-8, Interleukin-10, Interleukin-12 Subunit p40,Interleukin-12 Subunit p70, Interleukin-13, Interleukin-15,Interleukin-16, Leptin, Lymphotactin, Macrophage Inflammatory Protein-1alpha, Macrophage Inflammatory Protein-1 beta, Macrophage-DerivedChemokine, Matrix Metalloproteinase-2, Matrix Metalloproteinase-3,Matrix Metalloproteinase-9, Monocyte Chemotactic Protein 1,Myeloperoxidase, Myoglobin, Plasminogen Activator Inhibitor 1,Pregnancy- Associated Plasma Protein A, Prostate-Specific Antigen (inc.Free PSA), Prostatic Acid Phosphatase, Serum Amyloid P-Component, SerumGlutamic Oxaloacetic Transaminase, Sex Hormone-Binding Globulin, StemCell Factor, T-Cell-Specific Protein RANTES, Thrombopoietin,Thyroid-Stimulating Hormone, Thyroxine- Binding Globulin, Tissue Factor,Tissue Inhibitor of Metalloproteinases 1, Tumor Necrosis Factor alpha,Tumor Necrosis Factor beta, Tumor Necrosis Factor Receptor 2, VascularCell Adhesion Molecule-1, Vascular Endothelial Growth Factor, vonWillebrand Factor Neurological Alpha-1-Antitrypsin, Apolipoprotein A-I,Apolipoprotein A-II, Apolipoprotein B, Apolipoprotein C-I,Apolipoprotein H, Beta-2-Microglobulin, Betacellulin, Brain- DerivedNeurotrophic Factor, Calbindin, Cancer Antigen 125, CarcinoembryonicAntigen, CD5 Antigen-like, Complement C3, Connective Tissue GrowthFactor, Cortisol, Endothelin-1, Epidermal Growth Factor Receptor,Ferritin, Fetuin-A, Follicle-Stimulating Hormone, Haptoglobin,Immunoglobulin A, Immunoglobulin M, Intercellular Adhesion Molecule 1,Interleukin-6 Receptor, Interleukin-7, Interleukin-10, Interleukin-11,Interleukin-17, Kidney Injury Molecule-1, Luteinizing Hormone,Macrophage-Derived Chemokine, Macrophage Migration Inhibitory Factor,Macrophage Inflammatory Protein-1 alpha, Matrix Metalloproteinase-2,Monocyte Chemotactic Protein 2, Peptide YY, Prolactin, Prostatic AcidPhosphatase, Serotransferrin, Serum Amyloid P-Component, Sortilin,Testosterone, Thrombopoietin, Thyroid-Stimulating Hormone, TissueInhibitor of Metalloproteinases 1, TNF-Related Apoptosis-Inducing LigandReceptor 3, Tumor necrosis Factor Receptor 2, Vascular EndothelialGrowth Factor, Vitronectin Cardiovascular Adiponectin, ApolipoproteinA-I, Apolipoprotein B, Apolipoprotein C-III, Apolipoprotein D,Apolipoprotein E, Apolipoprotein H, Apolipoprotein(a), Clusterin,C-Reactive Protein, Cystatin-C, EN-RAGE, E-Selectin, Fatty Acid- BindingProtein (heart), Ferritin, Fibrinogen, Haptoglobin, Immunoglobulin M,Intercellular Adhesion Molecule 1, Interleukin-6, Interleukin-8,Lectin-Like Oxidized LDL Receptor 1, Leptin, Macrophage InflammatoryProtein-1 alpha, Macrophage Inflammatory Protein-1 beta,Malondialdehyde-Modified Low- Density Lipoprotein, MatrixMetalloproteinase-1, Matrix Metalloproteinase-10, MatrixMetalloproteinase-2, Matrix Metalloproteinase-3, MatrixMetalloproteinase-7, Matrix Metalloproteinase-9, Monocyte ChemotacticProtein 1, Myeloperoxidase, Myoglobin, NT-proBNP, Osteopontin,Plasminogen Activator Inhibitor 1, P-Selectin, Receptor for advancedglycosylation end products, Serum Amyloid P-Component, SexHormone-Binding Globulin, T-Cell- Specific Protein RANTES,Thrombomodulin, Thyroxine-Binding Globulin, Tissue Inhibitor ofMetalloproteinases 1, Tumor Necrosis Factor alpha, Tumor necrosis FactorReceptor 2, Vascular Cell Adhesion Molecule-1, von Willebrand FactorInflammatory Alpha-1-Antitrypsin, Alpha-2-Macroglobulin,Beta-2-Microglobulin, Brain- Derived Neurotrophic Factor, Complement C3,C-Reactive Protein, Eotaxin-1, Factor VII, Ferritin, Fibrinogen,Granulocyte-Macrophage Colony-Stimulating Factor, Haptoglobin,Intercellular Adhesion Molecule 1, Interferon gamma, Interleukin-1alpha, Interleukin-1 beta, Interleukin-1 Receptor antagonist,Interleukin-2, Interleukin-3, Interleukin-4, Interleukin-5,Interleukin-6, Interleukin-7, Interleukin-8, Interleukin-10,Interleukin-12 Subunit p40, Interleukin-12 Subunit p70, Interleukin-15,Interleukin-17, Interleukin-23, Macrophage Inflammatory Protein-1 alpha,Macrophage Inflammatory Protein-1 beta, Matrix Metalloproteinase-2,Matrix Metalloproteinase-3, Matrix Metalloproteinase-9, MonocyteChemotactic Protein 1, Stem Cell Factor, T-Cell- Specific ProteinRANTES, Tissue Inhibitor of Metalloproteinases 1, Tumor Necrosis Factoralpha, Tumor Necrosis Factor beta, Tumor necrosis Factor Receptor 2,Vascular Cell Adhesion Molecule-1, Vascular Endothelial Growth Factor,Vitamin D-Binding Protein, von Willebrand Factor Metabolic Adiponectin,Adrenocorticotropic Hormone, Angiotensin-Converting Enzyme,Angiotensinogen, Complement C3 alpha des arg, Cortisol,Follicle-Stimulating Hormone, Galanin, Glucagon, Glucagon-like Peptide1, Insulin, Insulin-like Growth Factor I, Leptin, Luteinizing Hormone,Pancreatic Polypeptide, Peptide YY, Progesterone, Prolactin, Resistin,Secretin, Testosterone Kidney Alpha-1-Microglobulin,Beta-2-Microglobulin, Calbindin, Clusterin, Connective Tissue GrowthFactor, Creatinine, Cystatin-C, Glutathione S-Transferase alpha, KidneyInjury Molecule-1, Microalbumin, Neutrophil Gelatinase-AssociatedLipocalin, Osteopontin, Tamm-Horsfall Urinary Glycoprotein, TissueInhibitor of Metalloproteinases 1, Trefoil Factor 3, VascularEndothelial Growth Factor Cytokines Granulocyte-MacrophageColony-Stimulating Factor, Interferon gamma, Interleukin-2,Interleukin-3, Interleukin-4, Interleukin-5, Interleukin-6,Interleukin-7, Interleukin-8, Interleukin-10, Macrophage InflammatoryProtein-1 alpha, Macrophage Inflammatory Protein-1 beta, MatrixMetalloproteinase-2, Monocyte Chemotactic Protein 1, Tumor NecrosisFactor alpha, Tumor Necrosis Factor beta, Brain-Derived NeurotrophicFactor, Eotaxin-1, Intercellular Adhesion Molecule 1, Interleukin-1alpha, Interleukin-1 beta, Interleukin-1 Receptor antagonist,Interleukin-12 Subunit p40, Interleukin-12 Subunit p70, Interleukin- 15,Interleukin-17, Interleukin-23, Matrix Metalloproteinase-3, Stem CellFactor, Vascular Endothelial Growth Factor Protein 14.3.3 gamma, 14.3.3(Pan), 14-3-3 beta, 6-Histidine, a-B-Crystallin, Acinus, Actin beta,Actin (Muscle Specific), Actin (Pan), Actin (skeletal muscle), ActivinReceptor Type II, Adenovirus, Adenovirus Fiber, Adenovirus Type 2 E1A,Adenovirus Type 5 E1A, ADP-ribosylation Factor (ARF-6),Adrenocorticotrophic Hormone, AIF (Apoptosis Inducing Factor), AlkalinePhosphatase (AP), Alpha Fetoprotein (AFP), Alpha Lactalbumin,alpha-1-antichymotrypsin, alpha-1- antitrypsin, Amphiregulin, AmylinPeptide, Amyloid A, Amyloid A4 Protein Precursor, Amyloid Beta (APP),Androgen Receptor, Ang-1, Ang-2, APC, APC11, APC2, Apolipoprotein D,A-Raf, ARC, Ask1/MAPKKK5, ATM, Axonal Growth Cones, b Galactosidase,b-2-Microglobulin, B7-H2, BAG-1, Bak, Bax, B-Cell, B-cell Linker Protein(BLNK), Bc110/CIPER/CLAP/mE10, bcl- 2a, Bcl-6, bcl-X, bcl-XL, Bim (BOD),Biotin, Bonzo/STRL33/TYMSTR, Bovine Serum Albumin, BRCA2 (aa 1323-1346),BrdU, Bromodeoxyuridine (BrdU), CA125, CA19-9, c-Abl, Cadherin (Pan),Cadherin-E, Cadherin-P, Calcitonin, Calcium Pump ATPase, Caldesmon,Calmodulin, Calponin, Calretinin, Casein, Caspase 1, Caspase 2, Caspase3, Caspase 5, Caspase 6 (Mch 2), Caspase 7 (Mch 3), Caspase 8 (FLICE),Caspase 9, Catenin alpha, Catenin beta, Catenin gamma, Cathepsin D,CCK-8, CD1, CD10, CD100/Leukocyte Semaphorin, CD105, CD106/VCAM,CD115/c-fms/CSF-1R/M-CSFR, CD137 (4-1BB), CD138, CD14, CD15, CD155/PVR(Polio Virus Receptor), CD16, CD165, CD18, CD1a, CD1b, CD2, CD20, CD21,CD23, CD231, CD24, CD25/IL-2 Receptor a, CD26/DPP IV, CD29, CD30(Reed-Sternberg Cell Marker), CD32/Fcg Receptor II, CD35/CR1,CD36GPIIIb/GPIV, CD3zeta, CD4, CD40, CD42b, CD43, CD45/T200/LCA, CD45RB,CD45RO, CD46, CD5, CD50/ICAM-3, CD53, CD54/ICAM-1, CD56/NCAM-1, CD57,CD59/MACIF/MIRL/Protectin, CD6, CD61/Platelet Glycoprotein IIIA, CD63,CD68, CD71/Transferrin Receptor, CD79a mb-1, CD79b, CD8, CD81/TAPA-1,CD84, CD9, CD94, CD95/Fas, CD98, CDC14A Phosphatase, CDC25C, CDC34,CDC37, CDC47, CDC6, cdh1, Cdk1/p34cdc2, Cdk2, Cdk3, Cdk4, Cdk5, Cdk7,Cdk8, CDw17, CDw60, CDw75, CDw78, CEA/CD66e, c-erbB-2/HER-2/neu Ab-1(21N), c-erbB-4/HER-4, c-fos, Chk1, Chorionic Gonadotropin beta(hCG-beta), Chromogranin A, CIDE-A, CIDE-B, CITED1, c-jun, Clathrin,claudin 11, Claudin 2, Claudin 3, Claudin 4, Claudin 5, CLAUDIN 7,Claudin-1, CNPase, Collagen II, Collagen IV, Collagen IX, Collagen VII,Connexin 43, COX2, CREB, CREB-Binding Protein, Cryptococcus neoformans,c-Src, Cullin-1 (CUL-1), Cullin-2 (CUL-2), Cullin-3 (CUL-3),CXCR4/Fusin, Cyclin B1, Cyclin C, Cyclin D1, Cyclin D3, Cyclin E, CyclinE2, Cystic Fibrosis Transmembrane Regulator, Cytochrome c, D4-GDI, Daxx,DcR1, DcR2/TRAIL-R4/TRUNDD, Desmin, DFF40 (DNA Fragmentation Factor40)/CAD, DFF45/ICAD, DJ-1, DNA Ligase I, DNA Polymerase Beta, DNAPolymerase Gamma, DNA Primase (p49), DNA Primase (p58), DNA-PKcs, DP-2,DR3, DRS, Dysferlin, Dystrophin, E2F-1, E2F-2, E2F-3, E2F-4, E2F-5,E3-binding protein (ARM1), EGFR, EMA/CA15-3/MUC-1, Endostatin,Epithelial Membrane Antigen (EMA/CA15-3/MUC-1), Epithelial SpecificAntigen, ER beta, ER Ca+2 ATPase2, ERCC1, Erk1, ERK2, Estradiol,Estriol, Estrogen Receptor, Exo1, Ezrin/p81/80K/Cytovillin, F.VIII/VWF,Factor VIII Related Antigen, FADD (FAS-Associated deathdomain-containing protein), Fascin, Fas-ligand, Ferritin, FGF-1, FGF-2,FHIT, Fibrillin-1, Fibronectin, Filaggrin, Filamin, FITC, Fli-1, FLIP,Flk-1/KDR/VEGFR2, Flt-1/VEGFR1, Flt-4, Fra2, FSH, FSH-b, Fyn, Ga0,Gab-1, GABA a Receptor 1, GAD65, Gai1, Gamma Glutamyl Transferase (gGT),Gamma Glutamylcysteine Synthetase(GCS)/Glutamate-cysteine Ligase, GAPDH,Gastrin 1, GCDFP-15, G- CSF, GFAP, Glicentin, Glucagon,Glucose-Regulated Protein 94, GluR 2/3, GluR1, GluR4, GluR6/7, GLUT-1,GLUT-3, Glycogen Synthase Kinase 3b (GSK3b), Glycophorin A, GM-CSF, GnRHReceptor, Golgi Complex, Granulocyte, Granzyme B, Grb2, GreenFluorescent Protein (GFP), GRIP1, Growth Hormone (hGH), GSK-3, GST,GSTmu, H.Pylori, HDAC1, HDJ- 2/DNAJ, Heat Shock Factor 1, Heat ShockFactor 2, Heat Shock Protein 27/hsp27, Heat Shock Protein 60/hsp60, HeatShock Protein 70/hsp70, Heat Shock Protein 75/hsp75, Heat Shock Protein90a/hsp86, Heat Shock Protein 90b/hsp84, Helicobacter pylori, HeparanSulfate Proteoglycan, Hepatic Nuclear Factor-3B, Hepatocyte, HepatocyteFactor Homologue-4, Hepatocyte Growth Factor, Heregulin, HIF-1a, HistoneH1, hPL, HPV 16, HPV 16-E7, HRP, Human Sodium Iodide Symporter (hNIS),I-FLICE/CASPER, IFN gamma, IgA, IGF-1R, IGF-I, IgG, IgM (m-Heavy Chain),I-Kappa-B Kinase b (IKKb), IL-1 alpha, IL-1 beta, IL-10, IL-10R, IL17,IL-2, IL-3, IL-30, IL-4, IL-5, IL-6, IL-8, Inhibin alpha, Insulin,Insulin Receptor, Insulin Receptor Substrate-1, Int-2 Oncoprotein,Integrin beta5, Interferon-a(II), Interferon-g, Involucrin, IP10/CRG2,IPO-38 Proliferation Marker, IRAK, ITK, JNK Activating kinase (JKK1),Kappa Light Chain, Keratin 10, Keratin 10/13, Keratin 14, Keratin 15,Keratin 16, Keratin 18, Keratin 19, Keratin 20, Keratin 5/6/18, Keratin5/8, Keratin 8, Keratin 8 (phospho- specific Ser73), Keratin 8/18,Keratin (LMW), Keratin (Multi), Keratin (Pan), Ki67, Ku (p70/p80), Ku(p80), L1 Cell Adhesion Molecule, Lambda Light Chain, Laminin B1/b1,Laminin B2/g1, Laminin Receptor, Laminin-s, Lck, Lck (p561ck),Leukotriene (C4, D4, E4), LewisA, LewisB, LH, L-Plastin, LRP/MVP,Luciferase, Macrophage, MADD, MAGE-1, Maltose Binding Protein, MAP1B,MAP2a,b, MART-1/Melan-A, Mast Cell Chymase, Mcl-1, MCM2, MCM5, MDM2,Medroxyprogesterone Acetate (MPA), Mek1, Mek2, Mek6, Mekk-1, Melanoma(gp100), mGluR1, mGluR5, MGMT, MHC I (HLA25 and HLA- Aw32), MHC I(HLA-A), MHC I (HLA-A,B,C), MHC I (HLA-B), MHC II (HLA-DP and DR), MHCII (HLA-DP), MHC II (HLA-DQ), MHC II (HLA-DR), MHC II (HLA-DR) Ia,Microphthalmia, Milk Fat Globule Membrane Protein, Mitochondria, MLH1,MMP-1 (Collagenase-I), MMP-10 (Stromilysin-2), MMP- 11 (Stromelysin-3),MMP-13 (Collagenase-3), MMP-14/MT1-MMP, MMP-15/ MT2-MMP, MMP-16/MT3-MMP,MMP-19, MMP-2 (72 kDa Collagenase IV), MMP-23, MMP-7 (Matrilysin), MMP-9(92 kDa Collagenase IV), Moesin, mRANKL, Muc-1, Mucin 2, Mucin 3 (MUC3),Mucin 5AC, MyD88, Myelin/ Oligodendrocyte, Myeloid Specific Marker,Myeloperoxidase, MyoD1, Myogenin, Myoglobin, Myosin Smooth Muscle HeavyChain, Nck, Negative Control for Mouse IgG1, Negative Control for MouseIgG2a, Negative Control for Mouse IgG3, Negative Control for Mouse IgM,Negative Control for Rabbit IgG, Neurofilament, Neurofilament (160 kDa),Neurofilament (200 kDa), Neurofilament (68 kDa), Neuron SpecificEnolase, Neutrophil Elastase, NF kappa B/p50, NF kappa B/p65 (Rel A),NGF-Receptor (p75NGFR), brain Nitric Oxide Synthase (bNOS), endothelialNitric Oxide Synthase (eNOS), nm23, NOS-i, NOS-u, Notch, Nucleophosmin(NPM), NuMA, O ct-1, Oct-2/, Oct-3/, Ornithine Decarboxylase,Osteopontin, p130, p130cas, p14ARF, p15INK4b, p16INK4a, p170, p170/MDR-1, p18INK4c, p19ARF, p19Skp1, p21WAF1, p27Kip1, p300/CBP, p35nck5a,P504S, p53, p57Kip2 Ab-7, p63 (p53 Family Member), p73, p73a, p73a/b,p95VAV, Parathyroid Hormone, Parathyroid Hormone Receptor Type 1,Parkin, PARP, PARP (Poly ADP-Ribose Polymerase), Pax-5, Paxillin, PCNA,PCTAIRE2, PDGF, PDGFR alpha, PDGFR beta, Pds1, Perforin, PGP9.5, PHAS-I, PHAS-II, Phospho-Ser/Thr/Tyr, Phosphotyrosine, PLAP, Plasma CellMarker, Plasminogen, PLC gamma 1, PMP-22, Pneumocystis jiroveci,PPAR-gamma, PR3 (Proteinase 3), Presenillin, Progesterone, ProgesteroneReceptor, Progesterone Receptor (phospho-specific) - Serine 190,Progesterone Receptor (phospho- specific) - Serine 294, Prohibitin,Prolactin, Prolactin Receptor, Prostate Apoptosis Response Protein-4,Prostate Specific Acid Phosphatase, Prostate Specific Antigen, pS2,PSCA, Rabies Virus, RAD1, Rad51, Raf1, Raf-1 (Phospho- specific), RAIDD,Ras, Rad18, Renal Cell Carcinoma, Ret Oncoprotein, Retinoblastoma,Retinoblastoma (Rb) (Phospho-specific Serine608), Retinoic Acid Receptor(b), Retinoid X Receptor (hRXR), Retinol Binding Protein, Rhodopsin(Opsin), ROC, RPA/p32, RPA/p70, Ruv A, Ruv B, Ruv C, 5100, S100A4,S100A6, SHP-1, SIM Ag (SIMA-4D3), SIRP a1, sm, SODD (Silencer of DeathDomain), Somatostatin Receptor-I, SRC1 (Steroid Receptor Coactivator-1)Ab-1, SREBP-1 (Sterol Regulatory Element Binding Protein-1), SRF (SerumResponse Factor), Stat-1, Stat3, Stat5, Stat5a, Stat5b, Stat6,Streptavidin, Superoxide Dismutase, Surfactant Protein A, SurfactantProtein B, Surfactant Protein B (Pro), Survivin, SV40 Large T Antigen,Syk, Synaptophysin, Synuclein, Synuclein beta, Synuclein pan, TACE(TNF-alpha converting enzyme)/ ADAM17, TAG-72, tau, TdT, Tenascin,Testosterone, TGF beta 3, TGF-beta 2, Thomsen-Friedenreich Antigen,Thrombospondin, Thymidine Phosphorylase, Thymidylate Synthase, ThymineGlycols, Thyroglobulin, Thyroid Hormone Receptor beta, Thyroid HormoneReceptor, Thyroid Stimulating Hormone (TSH), TID-1, TIMP-1, TIMP-2, TNFalpha, TNFa, TNR-R2, Topo II beta, Topoisomerase IIa, Toxoplasma Gondii,TR2, TRADD, Transforming Growth Factor a, Transglutaminase II, TRAP,Tropomyosin, TRP75/gp75, TrxR2, TTF- 1, Tubulin, Tubulin-a, Tubulin-b,Tyrosinase, Ubiquitin, UCP3, uPA, Urocortin, Vacular Endothelial GrowthFactor(VEGF), Vimentin, Vinculin, Vitamin D Receptor (VDR), vonHippel-Lindau Protein, Wnt-1, Xanthine Oxidase, XPA, XPF, XPG, XRCC1,XRCC2, ZAP-70, Zip kinase Known Cancer ABL1, ABL2, ACSL3, AF15Q14, AF1Q,AF3p21, AF5q31, AKAP9, AKT1, Genes AKT2, ALDH2, ALK, ALO17, APC,ARHGEF12, ARHH, ARID1A, ARID2, ARNT, ASPSCR1, ASXL1, ATF1, ATIC, ATM,ATRX, BAP1, BCL10, BCL11A, BCL11B, BCL2, BCL3, BCL5, BCL6, BCL7A, BCL9,BCOR, BCR, BHD, BIRC3, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRD3, BRD4,BRIP1, BTG1, BUB1B, C12orf9, C15orf21, C15orf55, C16orf75, CANT1,CARD11, CARS, CBFA2T1, CBFA2T3, CBFB, CBL, CBLB, CBLC, CCNB1IP1, CCND1,CCND2, CCND3, CCNE1, CD273, CD274, CD74, CD79A, CD79B, CDH1, CDH11,CDK12, CDK4, CDK6, CDKN2A, CDKN2a(p14), CDKN2C, CDX2, CEBPA, CEP1,CHCHD7, CHEK2, CHIC2, CHN1, CIC, CIITA, CLTC, CLTCL1, CMKOR1, COL1A1,COPEB, COX6C, CREB1, CREB3L1, CREB3L2, CREBBP, CRLF2, CRTC3, CTNNB1,CYLD, D10S170, DAXX, DDB2, DDIT3, DDX10, DDX5, DDX6, DEK, DICER1,DNMT3A, DUX4, EBF1, EGFR, EIF4A2, ELF4, ELK4, ELKS, ELL, ELN, EML4,EP300, EPS15, ERBB2, ERCC2, ERCC3, ERCC4, ERCC5, ERG, ETV1, ETV4, ETV5,ETV6, EVI1, EWSR1, EXT1, EXT2, EZH2, FACL6, FAM22A, FAM22B, FAM46C,FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FBXO11, FBXW7, FCGR2B, FEV,FGFR1, FGFR1OP, FGFR2, FGFR3, FH, FHIT, FIP1L1, FLI1, FLJ27352, FLT3,FNBP1, FOXL2, FOXO1A, FOXO3A, FOXP1, FSTL3, FUBP1, FUS, FVT1, GAS7,GATA1, GATA2, GATA3, GMPS, GNA11, GNAQ, GNAS, GOLGA5, GOPC, GPC3, GPHN,GRAF, HCMOGT-1, HEAB, HERPUD1, HEY1, HIP1, HIST1H4I, HLF, HLXB9, HMGA1,HMGA2, HNRNPA2B1, HOOK3, HOXA11, HOXA13, HOXA9, HOXC11, HOXC13, HOXD11,HOXD13, HRAS, HRPT2, HSPCA, HSPCB, IDH1, IDH2, IGH@, IGK@, IGL@, IKZF1,IL2, IL21R, IL6ST, IL7R, IRF4, IRTA1, ITK, JAK1, JAK2, JAK3, JAZF1, JUN,KDM5A, KDM5C, KDM6A, KDR, KIAA1549, KIT, KLK2, KRAS, KTN1, LAF4, LASP1,LCK, LCP1, LCX, LHFP, LIFR, LMO1, LMO2, LPP, LYL1, MADH4, MAF, MAFB,MALT1, MAML2, MAP2K4, MDM2, MDM4, MDS1, MDS2, MECT1, MED12, MEN1, MET,MITF, MKL1, MLF1, MLH1, MLL, MLL2, MLL3, MLLT1, MLLT10, MLLT2, MLLT3,MLLT4, MLLT6, MLLT7, MN1, MPL, MSF, MSH2, MSH6, MSI2, MSN, MTCP1, MUC1,MUTYH, MYB, MYC, MYCL1, MYCN, MYD88, MYH11, MYH9, MYST4, NACA, NBS1,NCOA1, NCOA2, NCOA4, NDRG1, NF1, NF2, NFE2L2, NFIB, NFKB2, NIN, NKX2-1,NONO, NOTCH1, NOTCH2, NPM1, NR4A3, NRAS, NSD1, NTRK1, NTRK3, NUMA1,NUP214, NUP98, OLIG2, OMD, P2RY8, PAFAH1B2, PALB2, PAX3, PAX5, PAX7,PAX8, PBRM1, PBX1, PCM1, PCSK7, PDE4DIP, PDGFB, PDGFRA, PDGFRB, PER1,PHOX2B, PICALM, PIK3CA, PIK3R1, PIM1, PLAG1, PML, PMS1, PMS2, PMX1,PNUTL1, POU2AF1, POU5F1, PPARG, PPP2R1A, PRCC, PRDM1, PRDM16, PRF1,PRKAR1A, PRO1073, PSIP2, PTCH, PTEN, PTPN11, RAB5EP, RAD51L1, RAF1,RALGDS, RANBP17, RAP1GDS1, RARA, RB1, RBM15, RECQL4, REL, RET, ROS1,RPL22, RPN1, RUNDC2A, RUNX1, RUNXBP2, SBDS, SDH5, SDHB, SDHC, SDHD,SEPT6, SET, SETD2, SF3B1, SFPQ, SFRS3, SH3GL1, SIL, SLC45A3, SMARCA4,SMARCB1, SMO, SOCS1, SOX2, SRGAP3, SRSF2, SS18, SS18L1, SSH3BP1, SSX1,SSX2, SSX4, STK11, STL, SUFU, SUZ12, SYK, TAF15, TAL1, TAL2, TCEA1,TCF1, TCF12, TCF3, TCF7L2, TCL1A, TCL6, TET2, TFE3, TFEB, TFG, TFPT,TFRC, THRAP3, TIF1, TLX1, TLX3, TMPRSS2, TNFAIP3, TNFRSF14, TNFRSF17,TNFRSF6, TOP1, TP53, TPM3, TPM4, TPR, TRA@, TRB@, TRD@, TRIM27, TRIM33,TRIP11, TSC1, TSC2, TSHR, TTL, U2AF1, USP6, VHL, VTI1A, WAS, WHSC1,WHSC1L1, WIF1, WRN, WT1, WTX, XPA, XPC, XPO1, YWHAE, ZNF145, ZNF198,ZNF278, ZNF331, ZNF384, ZNF521, ZNF9, ZRSR2 Known Cancer AR, androgenreceptor; ARPC1A, actin-related protein complex 2/3 subunit A; GenesAURKA, Aurora kinase A; BAG4, BCl-2 associated anthogene 4; BCl2l2,BCl-2 like 2; BIRC2, Baculovirus IAP repeat containing protein 2;CACNA1E, calcium channel voltage dependent alpha-1E subunit; CCNE1,cyclin E1; CDK4, cyclin dependent kinase 4; CHD1L, chromodomain helicaseDNA binding domain 1- like; CKS1B, CDC28 protein kinase 1B; COPS3, COP9subunit 3; DCUN1D1, DCN1 domain containing protein 1; DYRK2, dualspecificity tyrosine phosphorylation regulated kinase 2; EEF1A2,eukaryotic elongation transcription factor 1 alpha 2; EGFR, epidermalgrowth factor receptor; FADD, Fas-associated via death domain; FGFR1,fibroblast growth factor receptor 1, GATA6, GATA binding protein 6;GPC5, glypican 5; GRB7, growth factor receptor bound protein 7; MAP3K5,mitogen activated protein kinase kinase kinase 5; MED29, mediatorcomplex subunit 5; MITF, microphthalmia associated transcription factor;MTDH, metadherin; NCOA3, nuclear receptor coactivator 3; NKX2-1, NK2homeobox 1; PAK1, p21/CDC42/RAC1-activated kinase 1; PAX9, paired boxgene 9; PIK3CA, phosphatidylinositol-3 kinase catalytic a; PLA2G10,phopholipase A2, group X; PPM1D, protein phosphatase magnesium-dependent1D; PTK6, protein tyrosine kinase 6; PRKCI, protein kinase C iota;RPS6KB1, ribosomal protein s6 kinase 70 kDa; SKP2, s-phase kinaseassociated protein; SMURF1, sMAD specific E3 ubiquitin protein ligase 1;SHH, sonic hedgehog homologue; STARD3, sTAR- related lipid transferdomain containing protein 3; YWHAQ, tyrosine 3- monooxygenase/tryptophan5-monooxygenase activation protein, zeta isoform; ZNF217, zinc fingerprotein 217 Mitotic Related Aurora kinase A (AURKA); Aurora kinase B(AURKB); Baculoviral IAP repeat- Cancer Genes containing 5, survivin(BIRC5); Budding uninhibited by benzimidazoles 1 homolog (BUB1); Buddinguninhibited by benzimidazoles 1 homolog beta, BUBR1 (BUB1B); Buddinguninhibited by benzimidazoles 3 homolog (BUB3); CDC28 protein kinaseregulatory subunit 1B (CKS1B); CDC28 protein kinase regulatory subunit 2(CKS2); Cell division cycle 2 (CDC2)/CDK1 Cell division cycle 20 homolog(CDC20); Cell division cycle-associated 8, borealin (CDCA8); Centromereprotein F, mitosin (CENPF); Centrosomal protein 110 kDa (CEP110);Checkpoint with forkhead and ring finger domains (CHFR); Cyclin B1(CCNB1); Cyclin B2 (CCNB2); Cytoskeleton-associated protein 5(CKAP5/ch-TOG); Microtubule-associated protein RP/EB family member 1.End-binding protein 1, EB1 (MAPRE1); Epithelial cell transformingsequence 2 oncogene (ECT2); Extra spindle poles like 1, separase(ESPL1); Forkhead box M1 (FOXM1); H2A histone family, member X (H2AFX);Kinesin family member 4A (KIF4A); Kinetochore- associated 1 (KNTC1/ROD);Kinetochore-associated 2; highly expressed in cancer 1 (KNTC2/HEC1);Large tumor suppressor, homolog 1 (LATS1); Large tumor suppressor,homolog 2 (LATS2); Mitotic arrest deficient-like 1; MAD1 (MAD1L1);Mitotic arrest deficient-like 2; MAD2 (MAD2L1); Mps1 protein kinase(TTK); Never in mitosis gene a-related kinase 2 (NEK2); Ninein, GSK3binteracting protein (NIN); Non-SMC condensin I complex, subunit D2(NCAPD2/CNAP1); Non-SMC condensin I complex, subunit H (NACPH/CAPH);Nuclear mitotic apparatus protein 1 (NUMA1); Nucleophosmin (nucleolarphosphoprotein B23, numatrin); (NPM1); Nucleoporin (NUP98);Pericentriolar material 1 (PCM1); Pituitary tumor-transforming 1,securin (PTTG1); Polo-like kinase 1 (PLK1); Polo-like kinase 4(PLK4/SAK); Protein (peptidylprolyl cis/trans isomerase)NIMA-interacting 1 (PIN1); Protein regulator of cytokinesis 1 (PRC1);RAD21 homolog (RAD21); Ras association (RalGDS/AF-6); domain family 1(RASSF1); Stromal antigen 1 (STAG1); Synuclein-c, breast cancer-specificprotein 1 (SNCG, BCSG1); Targeting protein for Xklp2 (TPX2);Transforming, acidic coiled-coil containing protein 3 (TACC3);Ubiquitin-conjugating enzyme E2C (UBE2C); Ubiquitin-conjugating enzymeE2I (UBE2I/UBC9); ZW10 interactor, (ZWINT); ZW10, kinetochore-associated homolog (ZW10); Zwilch, kinetochore-associated homolog(ZWILCH) Ribonucleoprotein Argonaute family member, Ago1, Ago2, Ago3,Ago4, GW182 (TNRC6A), complexes TNRC6B, TNRC6C, HNRNPA2B1, HNRPAB, ILF2,NCL (Nucleolin), NPM1 (Nucleophosmin), RPL10A, RPL5, RPLP1, RPS12,RPS19, SNRPG, TROVE2, apolipoprotein, apolipoprotein A, apo A-I, apoA-II, apo A-IV, apo A-V, apolipoprotein B, apo B48, apo B100,apolipoprotein C, apo C-I, apo C-II, apo C- III, apo C-IV,apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), apolipoprotein L, APOL1, APOL2, APOL3, APOL4, APOL5, APOL6,APOLD1

The instant disclosure provides various biomarkers that can be assessedin determining a biosignature for a given test sample, and which includeassessment of polypeptides and/or nucleic acid biomarkers associatedwith various cancers, as well as the state of the cancer (e.g.,metastatic v. non-metastatic).

In one example, a test sample can be assessed for a cancer bydetermining the presence or level of one or more biomarker including butnot limited to CA-125, CA 19-9, and c-reactive protein. The cancer canbe a cancer of the reproductive tract, e.g., an ovarian cancer. The oneor more biomarker can further comprise one or more biomarkers, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 ormore biomarkers, comprising one or more of CD95, FAP-1, miR-200microRNAs, EGFR, EGFRvIII, apolipoprotein AI, apolipoprotein CIII,myoglobin, tenascin C, MSH6, claudin-3, claudin-4, caveolin-1,coagulation factor III, CD9, CD36, CD37, CD53, CD63, CD81, CD136, CD147,Hsp70, Hsp90, Rab13, Desmocollin-1, EMP-2, CK7, CK20, GCDF15, CD82,Rab-5b, Annexin V, MFG-E8 and HLA-DR. MiR-200 microRNAs (i.e., themiR-200 microRNA family) comprises miR-200a, miR-200b, miR-200c, miR-141and miR-429. Such assessment can include determining the presence orlevels of proteins, nucleic acids, or both for each of the biomarkersdisclosed herein.

CD95 (also called Fas, Fas antigen, Fas receptor, FasR, TNFRSF6, APT1 orAPO-1) is a prototypical death receptor that regulates tissuehomeostasis mainly in the immune system through the induction ofapoptosis. During cancer progression, CD95 is frequently downregulatedand the cells are rendered apoptosis resistant, thereby implicating lossof CD95 as part of a mechanism for tumour evasion. The tumorigenicactivity of CD95 is mediated by a pathway involving JNK and Jun. FAP-1(also referred to as Fas-associated phosphatase 1, protein tyrosinephosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associatedphosphatase), PTPN13) is a member of the protein tyrosine phosphatase(PTP) family. FAP-1 has been reported to interact with, anddephosphorylate, CD95, thereby implicating a role in Fas mediatedprogrammed cell death. MiR-200 family members can regulate CD95 andFAP-1. See Schickel et al. miR-200c regulates induction of apoptosisthrough CD95 by targeting FAP-1. Mol. Cell., 38, 908-915 (2010), whichpublication is incorporated by reference in its entirety herein.

Methods of the invention disclosed herein can use CD95 and/or FAP-1characterization or profiling for microvesicle populations present in abiological sample to determine the presence of or predisposition tocancer, including without limitation any of the cancers disclosedherein. Methods of the invention comprising multiplexed analysis formultiple biomarkers use CD95 and/or FAP-1 biomarker characterization,along with other biomarkers disclosed herein, including but not limitedto miR-200 microRNAs (e.g., miR-200c). In an embodiment, a biologicaltest sample from an individual is assessed to determine the presence andlevel of CD95 and/or FAP-1 protein, or a presence or level of a CD95+and/or FAP-1+ circulating microvesicle (“cMV”) population, and thepresence or levels are compared to a reference (e.g., samples fromnon-disease or normal, pre-treatment, or different treatmenttimepoints). This comparison is used to characterize the test sample.For example, comparison of the presence or levels of CD95 protein, FAP-1protein, CD95+cMVs and/or FAP-1+cMVs in the test sample and referenceare used to determine a disease phenotype or predict aresponse/non-response to treatment. In related embodiments, the cMVpopulation is further assessed to determine a presence or level ofmiR-200 microRNAs, which are predetermined in a training set ofreference samples to be indicative of disease or other prognostic,theranostic or diagnostic readout. Increased levels of FAP-1 in the testsample as compared to a non-cancer reference may indicate the presenceof a cancer, or the presence of a more aggressive cancer. Decreasedlevels of CD95 or miR200 family members such as miR-200c as compared toa non-cancer reference may indicate the presence of a cancer, or thepresence of a more aggressive cancer. The cMV population to be assessedcan be isolated through immunoprecipitation, flow cytometry, or otherisolation methodology disclosed herein or known in the art.

In a related aspect, the invention provides a method of characterizing acancer comprising detecting a level of one or more biomarker, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21or 22 biomarkers, selected from the group consisting of A2ML1, BAX,C10orf47, C1orf162, CSDA, EIFC3, ETFB, GABARAPL2, GUK1, GZMH, HIST1H3B,HLA-A, HSP90AA1, NRGN, PRDX5, PTMA, RABAC1, RABAGAP1L, RPL22, SAP18,SEPW1, SOX1, and a combination thereof. The one or more biomarker cancomprise PTMA (prothymosin, alpha), a member of the pro/parathymosinfamily which is cleaved into Thymosin alpha-1 and has a role in immunemodulation. Thymosin alpha-1 is approved in at least 35 countries forthe treatment of Hepatitis B and C, and it is also approved forinclusion with vaccines to boost the immune response in the treatment ofother diseases. In an embodiment, the biomarkers comprise mRNA. ThemRNAs can be isolated from vesicles that have been isolated as describedherein. In some embodiments, a total vesicle population in a sample isisolated, e.g., by filtration or centrifugation. The vesicles can alsoby isolated by affinity, e.g., using a binding agent to a generalvesicle biomarker, a disease biomarker or a cell-specific biomarker. Thelevels of the biomarkers can be compared to a control such as a samplewithout cancer, wherein a change between the levels of the biomarkersversus the control is used to characterize the cancer. The cancer can bea prostate cancer.

In an embodiment, the cancer assessed by the invention comprisesprostate cancer and microRNAs (miRs) are used to differentiate betweenmetastatic versus non-metastatic prostate cancer. Prostate cancerstaging is a process of categorizing the risk of cancer spread beyondthe prostate. Such spread is related to the probability of being curedwith local therapies such as surgery or radiation. The informationconsidered in such prognostic classification is based on clinical andpathological factors, including physical examination, imaging studies,blood tests and/or biopsy examination.

The most common scheme used to stage prostate cancer is promulgated bythe American Joint Committee on Cancer, and is referred to as the TNMsystem. The TNM system evaluates the size of the tumor, the extent ofinvolved lymph nodes, metastasis and also takes into account cancergrade. As with many other cancers, the cancers are often grouped bystage, e.g., stages I-IV). Generally, Stage I disease is cancer that isfound incidentally in a small part of the sample when prostate tissuewas removed for other reasons, such as benign prostatic hypertrophy, andthe cells closely resemble normal cells and the gland feels normal tothe examining finger. In Stage II more of the prostate is involved and alump can be felt within the gland. In Stage III, the tumor has spreadthrough the prostatic capsule and the lump can be felt on the surface ofthe gland. In Stage IV disease, the tumor has invaded nearby structures,or has spread to lymph nodes or other organs.

The Whitmore-Jewett stage is another staging scheme that is now usedless often. The Gleason Grading System is based on cellular content andtissue architecture from biopsies, which provides an estimate of thedestructive potential and ultimate prognosis of the disease.

The TNM tumor classification system can be used to describe the extentof cancer in a subject's body. T describes the size of the tumor andwhether it has invaded nearby tissue, N describes regional lymph nodesthat are involved, and M describes distant metastasis. TNM is maintainedby the International Union Against Cancer (UICC) and is used by theAmerican Joint Committee on Cancer (AJCC) and the InternationalFederation of Gynecology and Obstetrics (FIGO). Those of skill in theart understand that not all tumors have TNM classifications such as,e.g., brain tumors. Generally, T (a,is,(0), 1-4) is measured as the sizeor direct extent of the primary tumor. N (0-3) refers to the degree ofspread to regional lymph nodes: N0 means that tumor cells are absentfrom regional lymph nodes, N1 means that tumor cells spread to theclosest or small numbers of regional lymph nodes, N2 means that tumorcells spread to an extent between N1 and N3; N3 means that tumor cellsspread to most distant or numerous regional lymph nodes. M (0/1) refersto the presence of metastasis: MX means that distant metastasis was notassessed; M0 means that no distant metastasis are present; M1 means thatmetastasis has occurred to distant organs (beyond regional lymph nodes).M1 can be further delineated as follows: M1a indicates that the cancerhas spread to lymph nodes beyond the regional ones; M1b indicates thatthe cancer has spread to bone; and M1c indicates that the cancer hasspread to other sites (regardless of bone involvement). Other parametersmay also be assessed. G (1-4) refers to the grade of cancer cells (i.e.,they are low grade if they appear similar to normal cells, and highgrade if they appear poorly differentiated). R (0/1/2) refers to thecompleteness of an operation (i.e., resection-boundaries free of cancercells or not). L (0/1) refers to invasion into lymphatic vessels. V(0/1) refers to invasion into vein. C (1-4) refers to a modifier of thecertainty (quality) of V.

Prostate tumors are often assessed using the Gleason scoring system. TheGleason scoring system is based on microscopic tumor patterns assessedby a pathologist while interpreting a biopsy specimen. When prostatecancer is present in the biopsy, the Gleason score is based upon thedegree of loss of the normal glandular tissue architecture (i.e. shape,size and differentiation of the glands). The classic Gleason scoringsystem has five basic tissue patterns that are technically referred toas tumor “grades.” The microscopic determination of this loss of normalglandular structure caused by the cancer is represented by a grade, anumber ranging from 1 to 5, with 5 being the worst grade. Grade 1 istypically where the cancerous prostate closely resembles normal prostatetissue. The glands are small, well-formed, and closely packed. At Grade2 the tissue still has well-formed glands, but they are larger and havemore tissue between them, whereas at Grade 3 the tissue still hasrecognizable glands, but the cells are darker. At high magnification,some of these cells in a Grade 3 sample have left the glands and arebeginning to invade the surrounding tissue. Grade 4 samples have tissuewith few recognizable glands and many cells are invading the surroundingtissue. For Grade 5 samples, the tissue does not have recognizableglands, and are often sheets of cells throughout the surrounding tissue.

miRs that distinguish metastatic and non-metastatic prostate cancer canbe overexpressed in metastatic samples versus non-metastatic.Alternately, miRs that distinguish metastatic and non-metastaticprostate cancer can be overexpressed in non-metastatic samples versusmetastatic. Useful miRs for distinguishing metastatic prostate cancerinclude one or more, e.g., 1, 2, 3, 4, 5, 6, 7 or 8, miRs selected fromthe group consisting of miR-495, miR-10a, miR-30a, miR-570, miR-32,miR-885-3p, miR-564, and miR-134. In another embodiment, miRs fordistinguishing metastatic prostate cancer include one or more, e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14, miRs selected from thegroup consisting of hsa-miR-375, hsa-miR-452, hsa-miR-200b,hsa-miR-146b-5p, hsa-miR-1296, hsa-miR-17*, hsa-miR-100, hsa-miR-574-3p,hsa-miR-20a*, hsa-miR-572, hsa-miR-1236, hsa-miR-181a, hsa-miR-937, andhsa-miR-23a*. In still another embodiment, useful miRs fordistinguishing metastatic prostate cancer include, e.g., 1, 2, 3, 4, 5,6, 7, 8 or 9, miRs selected from the group consisting of hsa-miR-200b,hsa-miR-375, hsa-miR-582-3p, hsa-miR-17*, hsa-miR-1296, hsa-miR-20a*,hsa-miR-100, hsa-miR-452, and hsa-miR-577. The miRs for distinguishingmetastatic prostate cancer can be one or more, e.g., 1, 2, 3 or 4, miRsselected from the group consisting of miR-141, miR-375, miR-200b andmiR-574-3p.

In an aspect, microRNAs (miRs) are used to differentiate between cancerand non-cancer samples. Vesicles derived from patient samples can beanalyzed for miR payload contained within the vesicles. The sample canbe a bodily fluid, including semen, urine, blood, serum or plasma. Thesample can also comprise a tissue or biopsy sample. A number ofdifferent methodologies are available for detecting miRs. In someembodiments, arrays of miR panels are use to simultaneously query theexpression of multiple miRs. The Exiqon mIRCURY LNA microRNA PCR systempanel (Exiqon, Inc., Woburn, Mass.) can be used for such purposes. miRsthat distinguish cancer can be overexpressed in cancer versus controlsamples. Alternately, miRs that distinguish cancer can be overexpressedin cancer samples versus controls. Useful miRs for distinguishing cancerfrom non-cancer include one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12 or 13, miRs selected from the group consisting ofhsa-miR-574-3p, hsa-miR-331-3p, hsa-miR-326, hsa-miR-181a-2*,hsa-miR-130b, hsa-miR-301a, hsa-miR-141, hsa-miR-432, hsa-miR-107,hsa-miR-628-5p, hsa-miR-625*, hsa-miR-497, and hsa-miR-484. In anotherembodiment, useful miRs for distinguishing cancer from non-cancerinclude one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, miRsselected from the group consisting of hsa-miR-574-3p, hsa-miR-141,hsa-miR-331-3p, hsa-miR-432, hsa-miR-326, hsa-miR-2110, hsa-miR-107,hsa-miR-130b, hsa-miR-301a, and hsa-miR-625*. In still anotherembodiment, the useful miRs for distinguishing cancer from non-cancerinclude one or more, e.g., 1, 2, 3, 4, 5, 6, 7, 8 or 9, miRs selectedfrom the group consisting of hsa-miR-107, hsa-miR-326, hsa-miR-432,hsa-miR-574-3p, hsa-miR-625*, hsa-miR-2110, hsa-miR-301a, hsa-miR-141 orhsa-miR-373*. The cancer can comprise those cancers listed above. In anexemplary embodiment, the cancer is a prostate cancer and the microRNAs(miRs) are used to differentiate between prostate cancer and non-cancersamples.

The method contemplates assessing combinations of circulatingbiomarkers. For example, multiple markers from antibody arrays and miRanalysis can be used to distinguish prostate cancer from normal, BPH andPCa, or metastatic versus non-metastatic disease. In this manner,improved sensitivity, specificity, and/or accuracy can be obtained. Insome embodiments, the levels of one or more, e.g., 1, 2, 3, 4, 5 or 6,miRs selected from the group consisting of hsa-miR-432, hsa-miR-143,hsa-miR-424, hsa-miR-204, hsa-miR-581f and hsa-miR-451 are detected in apatient sample to assess the presence of prostate cancer. Any of thesemiRs can be elevated in patients with PCa but having serum PSA<4.0ng/ml. In an embodiment, the invention provides a method of assessing aprostate cancer, comprising determining a level of one or more, e.g., 1,2, 3, 4, 5 or 6, miRs selected from the group consisting of hsa-miR-432,hsa-miR-143, hsa-miR-424, hsa-miR-204, hsa-miR-581f and hsa-miR-451 in asample from a subject. The sample can be a bodily fluid, e.g., blood,plasma or serum. The miRs can be isolated in vesicles isolated from thesample. The subject can have a PSA level less than some threshold, suchas 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.2, 4.4, 4.6,4.8, 5.0, 5.2, 5.4, 5.6, 5.8, or 6.0 ng/ml in a blood sample. Higherlevels of the miRs than in a reference sample can indicate the presenceof PCa in the sample. In some embodiments, the reference comprises alevel of the one or more miRs in control samples from subjects withoutPCa. In some embodiments, the reference comprises a level of the one ormore miRs in control samples from subject with PCa and PSA levels≧somethreshold, such as 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8,4.0, 4.2, 4.4, 4.6, 4.8, 5.0, 5.2, 5.4, 5.6, 5.8, or 6.0 ng/ml. Thethreshold can be 4.0 ng/ml.

In some embodiments of the invention, vesicles in patient samples areassessed to provide a diagnostic, prognostic or theranostic readout.Vesicle analysis of patient samples includes the detection of vesiclesurface biomarkers, e.g., surface antigens, and/or vesicle payload,e.g., mRNAs and microRNAs, as described herein. Methods for analysis ofvesicles are presented in PCT Patent Application PCT/US09/06095,entitled “METHODS AND SYSTEMS OF USING EXOSOMES FOR DETERMININGPHENOTYPES” and filed Nov. 12, 2009; U.S. Provisional Patent Application61/362,674, entitled “METHODS AND SYSTEMS OF USING VESICLES FORDETERMINING PHENOTYPES” and filed Jul. 7, 2010; and U.S. ProvisionalPatent Application 61/393,823, entitled “DETECTION OF GI CANCERS” andfiled Oct. 15, 2010, which applications are incorporated by referenceherein in their entirety.

In one aspect, the invention includes a method of identifying abio-signature of one or more vesicles in a biological sample from saidsubject, wherein the bio-signature comprises analysis of vesicle surfaceantigens and vesicle payload. The surface antigens can comprise surfaceproteins and the vesicle payload can comprise microRNA. For example,vesicles can be captured using binding agents that recognize vesiclesurface antigens, and the microRNA inside these captured vesicles can beassessed. Accordingly, the bio-signature may comprise the surfaceantigens used for capture as well as the microRNA inside the vesicles.The bio-signature can be used for diagnostic, prognostic or theranosticpurposes. For example, the bio-signature can be a signature thatidentifies cancer, identifies aggressive or metastatic cancer, oridentifies a cancer that is likely to respond to a candidate therapeuticagent.

As an illustrative example, consider a method of capturing vesicles in asample using an antibody to B7H3 and then assessing the levels ofmiR-141 within the captured vesicles. In this example, the bio-signaturecomprises the level of miR-141 within exosomes displaying B7H3 on theirsurface. Depending on the levels of B7H3+ vesicles in the sample as wellas the levels of miR-141 within the sample, the bio-signature mayindicate that the sample contains a cancer, contains an aggressivecancer, is likely to respond to a certain chemotherapeutic agent, etc.

In one embodiment, the method of assessing cancer in a subjectcomprises: identifying a bio-signature of one or more vesicles in abiological sample from said subject, comprising: determining a level ofone or more general vesicles protein biomarkers; determining a level ofone or more cell-specific protein biomarkers; determining a level of oneor more disease-specific protein biomarkers; and determining the levelof one or more microRNA biomarkers in the vesicles, wherein saidcharacterizing comprises comparing said levels of biomarkers in saidsample to a reference to determine whether said subject may bepredisposed to or afflicted with cancer. The protein biomarkers can bedetected in a multiplex fashion in a single assay. The microRNAbiomarkers can also be detected in a multiplex fashion in a singleassay. In some cases, the cell-specific and disease-specific biomarkermay overlap, e.g., one biomarker may serve to identify a cancer from aparticular cellular origin. The biological sample can be a bodily fluid,such as blood, serum or plasma.

In an example, the method of the invention comprises a diagnostic testfor prostate cancer comprising isolating vesicles from a blood samplefrom a patient to detect vesicles indicative of the presence or absenceof prostate cancer. The blood can be serum or plasma. The vesicles areisolated by capture with “capture antibodies” that recognize specificvesicle surface antigens. The surface antigens for the prostate cancerdiagnostic assay include the tetraspanins CD9, CD63 and CD81, which aregenerally present on vesicles in the blood and therefore act as generalvesicle biomarkers, the prostate specific biomarkers PSMA and PCSA, andthe cancer specific biomarker B7H3. In some cases, EpCam is used as acancer specific biomarker as well or instead of B7H3. The captureantibodies can be tethered to a substrate. In an embodiment, thesubstrate comprises fluorescently labeled beads, wherein the beads aredifferentially labeled for each capture antibody. As desired, thepayload of the detected vesicles can be assessed in order tocharacterize the cancer.

As described above, the biomarkers of the invention can be assessed toidentify a biosignature. In an aspect, the invention provides a methodcomprising: determining a presence or level of one or more biomarker ina biological sample, wherein the one or more biomarker comprises one ormore biomarker selected from Table 5; and identifying a biosignaturecomprising the presence or level of the one or more biomarker. In someembodiments, the method further comprises comparing the biosignature toa reference biosignature, wherein the comparison is used to characterizea cancer, including the cancers disclosed herein or known in the art.The reference biosignature can be from a subject without the cancer. Thereference biosignature can also be from the subject, e.g., from normaladjacent tissue or from a sample taken at another point in time. Variousways of characterizing a cancer are disclosed herein. For example,characterizing the cancer may comprise identifying the presence or riskof the cancer in a subject, or identifying the cancer in a subject asmetastatic or aggressive. The comparing step comprises determiningwhether the biosignature is altered relative to the referencebiosignature, thereby providing a prognostic, diagnostic or theranosticcharacterization for the cancer. The biological sample comprises abodily fluid, including without limitation the bodily fluids disclosedherein. For example, the bodily fluid may comprise urine, blood or ablood derivative.

The one or more biomarker can be one or more biomarker, e.g., 1, 2, 3,4, 5, 6, 7, 8, 9 or 10 or more, selected from the group consisting ofmiR-22, let7a, miR-141, miR-182, miR-663, miR-155, mirR-125a-5p,miR-548a-5p, miR-628-5p, miR-517*, miR-450a, miR-920, hsa-miR-619,miR-1913, miR-224*, miR-502-5p, miR-888, miR-376a, miR-542-5p, miR-30b*,miR-1179, and a combination thereof. In an embodiment, the one or morebiomarker is selected from the group consisting of miR-22, let7a,miR-141, miR-920, miR-450a, and a combination thereof. The one or morebiomarker, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more, may be amessenger RNA (mRNA) selected from the group consisting of the genes inany of Tables 20-24 herein, and a combination thereof. For example, theone or more biomarker may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 ormore messenger RNA (mRNA) selected from the group consisting of A2ML1,BAX, C10orf47, C1orf162, CSDA, EIFC3, ETFB, GABARAPL2, GUK1, GZMH,HIST1H3B, HLA-A, HSP90AA1, NRGN, PRDX5, PTMA, RABAC1, RABAGAP1L, RPL22,SAP18, SEPW1, SOX1, and a combination thereof. The one or more biomarkermay comprise 1, 2, 3, 4, 5, or 6 messenger RNA (mRNA) selected from thegroup consisting of A2ML1, GABARAPL2, PTMA, RABAC1, SOX1, EFTB, and acombination thereof. The one or more biomarker may be isolated aspayload of a population of microvesicles. The population can be a totalpopulation of microvesicles from the sample or a specific population,such as a PCSA+ population. In an embodiment, the method is used toassess a prostate cancer. For example, the method can be used todistinguish a sample comprising prostate cancer from a sample withoutprostate cancer.

In an embodiment, the one or more biomarker, e.g., 1, 2, 3, 4, 5, 6, 7,8, 9 or 10 or more biomarkers, is selected from the group consisting ofCA-125, CA 19-9, c-reactive protein, CD95, FAP-1, EGFR, EGFRvIII,apolipoprotein AI, apolipoprotein CIII, myoglobin, tenascin C, MSH6,claudin-3, claudin-4, caveolin-1, coagulation factor III, CD9, CD36,CD37, CD53, CD63, CD81, CD136, CD147, Hsp70, Hsp90, Rab13,Desmocollin-1, EMP-2, CK7, CK20, GCDF15, CD82, Rab-5b, Annexin V,MFG-E8, HLA-DR, a miR200 microRNA, miR-200c, and a combination thereof.The one or more biomarker may comprise 1, 2, 3, 4 or 5 biomarkerselected from the group consisting of CA-125, CA 19-9, c-reactiveprotein, CD95, FAP-1, and a combination thereof. The one or morebiomarker may be isolated directly from sample, or as surface antigensor payload of a population of microvesicles. In an embodiment, themethod is used to assess an ovarian cancer. For example, the method canbe used to distinguish a sample comprising ovarian cancer from a samplewithout ovarian cancer. Alternately, the method can be used todistinguish amongst ovarian cancer having different stage or prognosis.

In another embodiment, the one or more biomarker, e.g., 1, 2, 3, 4, 5,6, 7, 8, 9 or 10 or more biomarkers, is selected from the groupconsisting of hsa-miR-574-3p, hsa-miR-141, hsa-miR-432, hsa-miR-326,hsa-miR-2110, hsa-miR-181a-2*, hsa-miR-107, hsa-miR-301a, hsa-miR-484,hsa-miR-625*, and a combination thereof. The method can be used toassess a prostate cancer. For example, the method can be used todistinguish a sample comprising prostate cancer from a sample withoutprostate cancer. In still another embodiment, the one or more biomarker,e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more biomarkers, is selectedfrom the group consisting of hsa-miR-582-3p, hsa-miR-20a*, hsa-miR-375,hsa-miR-200b, hsa-miR-379, hsa-miR-572, hsa-miR-513a-5p, hsa-miR-577,hsa-miR-23a*, hsa-miR-1236, hsa-miR-609, hsa-miR-17*, hsa-miR-130b,hsa-miR-619, hsa-miR-624*, hsa-miR-198, and a combination thereof. Forexample, the method can be used to distinguish a sample comprisingmetastatic prostate cancer from a sample with non-metastatic prostatecancer. The one or more biomarker may be isolated as payload of apopulation of microvesicles.

The one or more biomarker may be miR-497. The method can be used toassess a lung cancer. For example, the method can be used to distinguisha lung cancer sample from a non-cancer sample. The one or more biomarkermay be isolated as payload of a population of microvesicles.

The one or more biomarker, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or morebiomarkers, may comprise a messenger RNA (mRNA) selected from the groupconsisting of AQP2, BMP5, C16orf86, CXCL13, DST, ERCC1, GNAO1, KLHL5,MAP4K1, NELL2, PENK, PGF, POU3F1, PRSS21, SCML1, SEMG1, SMARCD3, SNAI2,TAF1C, TNNT3, and a combination thereof. The mRNA may be isolated frommicrovesicles. The method can be used to characterize a prostate cancer,such as distinguish a prostate cancer sample from a normal samplewithout cancer. In another embodiment, the one or more biomarker, e.g.,1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more biomarkers, comprises amessenger RNA (mRNA) selected from the group consisting of ADRB2, ARG2,C22orf32, CYorf14, EIF1AY, FEV, KLK2, KLK4, LRRC26, MAOA, NLGN4Y,PNPLA7, PVRL3, SIM2, SLC30A4, SLC45A3, STX19, TRIM36, TRPM8, and acombination thereof. The mRNA may be isolated from microvesicles. Themethod can be used to characterize a prostate cancer, such asdistinguish a prostate cancer sample from a sample having anothercancer, e.g., a breast cancer. In still another embodiment, the one ormore biomarker, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or morebiomarkers, comprises a messenger RNA (mRNA) selected from the groupconsisting of ADRB2, BAIAP2L2, C19orf33, CDX1, CEACAM6, EEF1A2, ERN2,FAM110B, FOXA2, KLK2, KLK4, LOC389816, LRRC26, MIPOL1, SLC45A3, SPDEF,TRIM31, TRIM36, ZNF613, and a combination thereof. The mRNA may beisolated from microvesicles. The method can be used to characterize aprostate cancer, such as distinguish a prostate cancer sample from asample having another cancer, e.g., a colorectal cancer. In yet anotherembodiment, the one or more biomarker, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9or 10 or more biomarkers, comprises a messenger RNA (mRNA) selected fromthe group consisting of ASTN2, CAB39L, CRIP1, FAM110B, FEV, GSTP1, KLK2,KLK4, LOC389816, LRRC26, MUC1, PNPLA7, SIM2, SLC45A3, SPDEF, TRIM36,TRPV6, ZNF613, and a combination thereof. The mRNA may be isolated frommicrovesicles. The method can be used to characterize a prostate cancer,such as distinguish a prostate cancer sample from a sample havinganother cancer, e.g., a lung cancer. The one or more biomarker can alsobe a microRNA that regulates one or more of the mRNAs used tocharacterize a prostate cancer. For example, the one or more biomarker,e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more biomarkers, may comprise amicroRNA selected from the group consisting of miRs-26a+b, miR-15,miR-16, miR-195, miR-497, miR-424, miR-206, miR-342-5p, miR-186,miR-1271, miR-600, miR-216b, miR-519 family, miR-203, and a combinationthereof. The microRNA can be assessed as payload of a microvesiclepopulation.

The invention also provides a method of identifying a biosignature byassessing biomarker complexes. In an aspect, the method comprisesisolating one or more nucleic acid-protein complex from a biologicalsample; determining a presence or level of one or more nucleic acidbiomarker with the one or more nucleic acid-protein complex; andidentifying a biosignature comprising the presence or level of the oneor more nucleic acid biomarker. In some embodiments, the biosignaturemay also comprise the presence or level of one or more protein or othercomponent of the complex. The nucleic acid-protein complex may beisolated from the biological sample using methodology disclosed hereinor known in the art. For example, the complex may be isolated byaffinity selection such as by immunoprecipitation, column chromatographyor flow cytometry, using a binding agent to a component of the complex.Binding agents can be as described herein, e.g., an antibody or aptamerto a protein component of the complex. In some embodiments, the methodfurther comprises comparing the biosignature to a referencebiosignature, wherein the comparison is used to characterize a cancer,including the cancers disclosed herein or known in the art. Thereference biosignature can be from a subject without the cancer. Thereference biosignature can also be from the subject, e.g., from normaladjacent tissue or from a sample taken at another point in time. Variousways of characterizing a cancer are disclosed herein. For example,characterizing the cancer may comprise identifying the presence or riskof the cancer in a subject, or identifying the cancer in a subject asmetastatic or aggressive. The comparing step comprises determiningwhether the biosignature is altered relative to the referencebiosignature, thereby providing a prognostic, diagnostic or theranosticcharacterization for the cancer. The biological sample comprises abodily fluid, including without limitation the bodily fluids disclosedherein. For example, the bodily fluid may comprise urine, blood or ablood derivative.

In an embodiment, the nucleic acid-protein complex comprises one or moreprotein, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more proteins,selected from the group consisting of one or more Argonaute familymember, Ago1, Ago2, Ago3, Ago4, GW182 (TNRC6A), TNRC6B, TNRC6C,HNRNPA2B1, HNRPAB, ILF2, NCL (Nucleolin), NPM1 (Nucleophosmin), RPL10A,RPL5, RPLP1, RPS12, RPS19, SNRPG, TROVE2, apolipoprotein, apolipoproteinA, apo A-I, apo A-II, apo A-IV, apo A-V, apolipoprotein B, apo B48, apoB100, apolipoprotein C, apo C-I, apo C-II, apo C-III, apo C-IV,apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), apolipoprotein L, APOL1, APOL2, APOL3, APOL4, APOL5, APOL6,APOLD1, and a combination thereof. For example, the nucleic acid-proteincomplex may comprise one or more protein selected from the groupconsisting of one or more Argonaute family member, Ago 1, Ago2, Ago3,Ago4, GW182 (TNRC6A), and a combination thereof. The nucleicacid-protein complex comprises one or more protein selected from thegroup consisting of Ago2, Apolipoprotein I, GW182 (TNRC6A), and acombination thereof.

In embodiments, the one or more nucleic acid in the nucleic acid-proteincomplex comprises one or more microRNA. For example, the one or moremicroRNA, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50 or moremicroRNA, can be a microRNA in Table 5. The one or more microRNA maycomprise one or more microRNA, e.g., 1, 2, 3, 4, 5 or 6 microRNA,selected from the group consisting of miR-22, miR-16, miR-148a, miR-92a,miR-451, let7a, and a combination thereof. The one or more microRNA maybe assessed in order to characterize, e.g., diagnose, prognose ortheranose, a cancer including without limitation a prostate cancer.

In an embodiment, the nucleic acid-protein complex comprises one or moreprotein selected from the group consisting of Ago2, Apolipoprotein I,GW182 (TNRC6A), and a combination thereof; and the one or more microRNAcomprises one or more microRNA selected from the group consisting ofmiR-16 and miR-92a, and a combination thereof. The one or more microRNAmay be assessed in order to characterize a prostate cancer.

The invention further provides a method of determining a biosignaturecomprising detecting nucleic acids in microvesicle population ofinterest. The vesicle population can be a whole population in abiological sample, or a subpopulation such as a subpopulation havingcertain surface antigens. The method comprises detecting one or moreprotein biomarker in a microvesicle population from a biological sample;determining a presence or level of one or more one or more nucleic acidbiomarker associated with the detected microvesicle population; andidentifying a biosignature comprising the presence or level of the oneor more nucleic acid. Techniques for detecting microvesicle populations,detecting proteins, and assessing nucleic acids can be disclosed hereinor as known in the art. For example, the microvesicles can be isolatedby affinity selection against the one or more protein, and nucleic acidcan be isolated from the selected microvesicles. The level of the one ormore one or more nucleic acid biomarker can be normalized to the levelof the one or more protein biomarker or to the level of the microvesiclepopulation. In some embodiments, the method further comprises comparingthe biosignature to a reference biosignature, wherein the comparison isused to characterize a cancer, including the cancers disclosed herein orknown in the art. The reference biosignature can be from a subjectwithout the cancer. The reference biosignature can also be from thesubject, e.g., from normal adjacent tissue or from a sample taken atanother point in time. Various ways of characterizing a cancer aredisclosed herein. For example, characterizing the cancer may compriseidentifying the presence or risk of the cancer in a subject, oridentifying the cancer in a subject as metastatic or aggressive. Thecomparing step comprises determining whether the biosignature is alteredrelative to the reference biosignature, thereby providing a prognostic,diagnostic or theranostic characterization for the cancer. Thebiological sample comprises a bodily fluid, including without limitationthe bodily fluids disclosed herein. For example, the bodily fluid maycomprise urine, blood or a blood derivative.

The proteins used for detecting one or more protein biomarker in amicrovesicle population may comprise one or more biomarker disclosedherein, such as in Tables 3-5 or 9-11. For example, the one or moreprotein can be selected from the group consisting of PCSA, Ago2, CD9 anda combination thereof. For example, the one or more protein can be PCSA,Ago2, CD9, PCSA and Ago2, PCSA and CD9, Ago2 and CD9, or all of PCSA,Ago2 and CD9. Another general vesicle marker such as in Table 3, e.g., atetraspanin such as CD63 or CD81 can be substituted for or used inaddition to CD9. Such multiple biomarkers can be used to identify amicrovesicle population having a certain origin. E.g., PCSA can identifyprostate-derived vesicles while CD9 identifies vesicles apart fromcellular debris. PCSA, PSMA, PSCA, KLK2 or PBP (prostate bindingprotein) can be used as a biomarker to characterize a prostate cancer.

The one or more nucleic acid biomarker may comprise one or more nucleicacid disclosed herein, such as in Table 5. In an embodiment, the one ormore nucleic acid comprises one or more microRNA. For example, the oneor more microRNA can be selected from 1, 2, 3, 4, 5 or 6 of miR-22,miR-16, miR-148a, miR-92a, miR-451, and let7a. In an embodiment, the oneor more protein biomarker comprises PCSA and Ago2; and the one or morenucleic acid biomarker comprises miR-22. In another embodiment, the oneor more protein biomarker comprises PCSA and/or CD9; and the one or morenucleic acid biomarker comprises miR-22. The method can be used tocharacterize a cancer such as a prostate cancer, e.g., to distinguish acancer sample from a non-cancer sample.

In other embodiments, the one or more nucleic acid comprises mRNA. mRNAcan be assessed as payload within microvesicles. For example, the one ormore nucleic acid biomarker comprises a messenger RNA (mRNA) selectedfrom Table 5. The mRNA may also be selected from any of Tables 22-24. Insome embodiments, the one or more protein biomarker comprises PCSA; andthe one or more nucleic acid biomarker comprises a messenger RNA (mRNA)selected from any of Tables 22-24. The method can be used tocharacterize a cancer such as a prostate cancer, e.g., to distinguish acancer sample from a non-cancer sample.

The level of the one or more one or more nucleic acid biomarker can benormalized to the level of the one or more protein biomarker. In anembodiment, the biosignature comprises a score calculated from a ratioof the level of the one or more protein biomarker and one or morenucleic acid biomarker. For example, the level of the nucleic acids canbe divided by the level of the proteins.

The score can be calculated from multiple proteins and multiple nucleicacids. In an embodiment, the one or more protein biomarker comprisesPCSA and PSMA and the one or more nucleic acid biomarker comprisesmiR-22 and let7a. The method is used to characterize a prostate cancer,e.g., to distinguish a prostate cancer sample from a non-prostate cancersample. The score may comprise taking the sum of: a) a first multiple ofthe level of miR-22 payload in the microvesicle subpopulation divided bythe level of PCSA protein associated with the microvesiclesubpopulation; b) a second multiple of the level of let7a payload in themicrovesicle subpopulation divided by the level of PCSA proteinassociated with the microvesicle subpopulation; and c) a third multipleof the level of PSMA protein associated with the microvesiclesubpopulation. The first, second and third multiples can be chosen tomaximize the ability of the method to distinguish the prostate cancer.For example, the multiple can be about 0.0001, 0.001, 0.01, 0.1, 0.5, 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 100, 1000 or 10000. In an embodiment, thefirst multiple is 10, the second multiple is 10, and the third multipleis 1. The score can be an average of the sum as:

Score=Average(10*miR22/PCSA MFI, 10*let-7a/PCSA MFI, PSMA MFI)

One of skill will appreciate that calculating the score may comprise amonotonic transformation of the sum. A similar scoring equation can bedeveloped for other biomarkers in other settings, such as usingalternate biomarkers to characterize other cancers.

By selecting a proper reference sample for comparison, the biosignaturesidentified can provide a diagnostic readout (e.g., reference sample isnormal or non-disease), prognostic (e.g., reference sample is for pooror good disease outcome, aggressiveness or the like), or theranostic(e.g., reference sample is from a cohort responsive or non-responsive toselected treatment).

Additional biomarkers that can be used in the methods of the inventioninclude those disclosed in International Patent ApplicationPCT/US2012/025741, filed Feb. 17, 2012; International Patent ApplicationPCT/US2011/048327, filed Aug. 18, 2011; International Patent ApplicationPCT/US2011/026750, filed Mar. 1, 2011; and International PatentApplication PCT/US2011/031479, filed Apr. 6, 2011; each of which isincorporated by reference herein in its entirety.

Gene Fusions

The one or more biomarkers assessed of vesicle, can be a gene fusion. Afusion gene is a hybrid gene created by the juxtaposition of twopreviously separate genes. This can occur by chromosomal translocationor inversion, deletion or via trans-splicing. The resulting fusion genecan cause abnormal temporal and spatial expression of genes, such asleading to abnormal expression of cell growth factors, angiogenesisfactors, tumor promoters or other factors contributing to the neoplastictransformation of the cell and the creation of a tumor. Such fusiongenes can be oncogenic due to the juxtaposition of: 1) a strong promoterregion of one gene next to the coding region of a cell growth factor,tumor promoter or other gene promoting oncogenesis leading to elevatedgene expression, or 2) due to the fusion of coding regions of twodifferent genes, giving rise to a chimeric gene and thus a chimericprotein with abnormal activity.

An example of a fusion gene is BCR-ABL, a characteristic molecularaberration in ˜90% of chronic myelogenous leukemia (CML) and in a subsetof acute leukemias (Kurzrock et al., Annals of Internal Medicine 2003;138(10):819-830). The BCR-ABL results from a translocation betweenchromosomes 9 and 22. The translocation brings together the 5′ region ofthe BCR gene and the 3′ region of ABL1, generating a chimeric BCR-ABL1gene, which encodes a protein with constitutively active tyrosine kinaseactivity (Mittleman et al., Nature Reviews Cancer 2007; 7(4):233-245).The aberrant tyrosine kinase activity leads to de-regulated cellsignaling, cell growth and cell survival, apoptosis resistance andgrowth factor independence, all of which contribute to thepathophysiology of leukemia (Kurzrock et al., Annals of InternalMedicine 2003; 138(10):819-830).

Another fusion gene is IGH-MYC, a defining feature of ˜80% of Burkitt'slymphoma (Ferry et al. Oncologist 2006; 11(4):375-83). The causal eventfor this is a translocation between chromosomes 8 and 14, bringing thec-Myc oncogene adjacent to the strong promoter of the immunoglobin heavychain gene, causing c-myc overexpression (Mittleman et al., NatureReviews Cancer 2007; 7(4):233-245). The c-myc rearrangement is a pivotalevent in lymphomagenesis as it results in a perpetually proliferativestate. It has wide ranging effects on progression through the cellcycle, cellular differentiation, apoptosis, and cell adhesion (Ferry etal. Oncologist 2006; 11(4):375-83).

A number of recurrent fusion genes have been catalogued in the Mittlemandatabase (cgap.nci.nih.gov/Chromosomes/Mitelman) and can be assessed ina vesicle, and used to characterize a phenotype. The gene fusion can beused to characterize a hematological malignancy or epithelial tumor. Forexample, TMPRSS2-ERG, TMPRSS2-ETV and SLC45A3-ELK4 fusions can bedetected and used to characterize prostate cancer; and ETV6-NTRK3 andODZ4-NRG1 for breast cancer.

Furthermore, assessing the presence or absence, or expression level of afusion gene can be used to diagnosis a phenotype such as a cancer aswell as a monitoring a therapeutic response to selecting a treatment.For example, the presence of the BCR-ABL fusion gene is a characteristicnot only for the diagnosis of CML, but is also the target of theNovartis drug Imatinib mesylate (Gleevec), a receptor tyrosine kinaseinhibitor, for the treatment of CML. Imatinib treatment has led tomolecular responses (disappearance of BCR-ABL+ blood cells) and improvedprogression-free survival in BCR-ABL+CML patients (Kantarjian et al.,Clinical Cancer Research 2007; 13(4):1089-1097).

Assessing a vesicle for the presence, absence, or expression level of agene fusion can be of by assessing a heterogeneous population ofvesicles for the presence, absence, or expression level of a genefusion. Alternatively, the vesicle that is assessed can be derived froma specific cell type, such as cell-of-origin specific vesicle, asdescribed above. Illustrative examples of use of fusions that can beassessed to characterize a phenotype include those described inInternational Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein.

Gene-Associated MiRNA Biomarkers

Illustrative examples of use of miRNA biomarkers known to interact withcertain transcripts and that can be assessed to characterize a phenotypeinclude those described in International Patent Application Serial No.PCT/US2011/031479, entitled “Circulating Biomarkers for Disease” andfiled Apr. 6, 2011, which application is incorporated by reference inits entirety herein.

Nucleic Acid—Protein Complex Biomarkers

MicroRNAs in human plasma have been found associated with circulatingmicrovesicles, Argonaute proteins, and HDL and LDL complexes. See, e.g.,Arroyo et al., Argonaute2 complexes carry a population of circulatingmicroRNAs independent of vesicles in human plasma. Proc Natl Acad SciUSA. 2011. 108:5003-08. Epub 2011 Mar. 7; Collino et al., Microvesiclesderived from adult human bone marrow and tissue specific mesenchymalstem cells shuttle selected pattern of miRNAs. PLOS One. 20105(7):e11803. The Argonaute family of proteins plays a role in RNAinterference (RNAi) gene silencing. Argonaute proteins bind short RNAssuch as microRNAs (miRNAs) or short interfering RNAs (siRNAs), andrepress the translation of their complementary mRNAs. They are alsoinvolved in transcriptional gene silencing (TGS), in which short RNAsknown as antigene RNAs or agRNAs direct the transcriptional repressionof complementary promoter regions. Argonaute family members includeArgonaute 1 (“eukaryotic translation initiation factor 2C, 1”, EIF2C1,AGO1), Argonaute 2 (“eukaryotic translation initiation factor 2C, 2”,EIF2C2, AGO2), Argonaute 3 (“eukaryotic translation initiation factor2C, 3”, EIF2C3, AGO3), and Argonaute 4 (“eukaryotic translationinitiation factor 2C, 4”, EIF2C4, AGO4). Several Argonaute isotypes havebeen identified. Argonaute 2 is an effector protein within theRNA-Induced Silencing Complex (RISC) where it plays a role in thesilencing of target messenger RNAs in the microRNA silencing pathway.

The protein GW182 associates with microvesicles and also has thecapacity to bind all human Argonaute proteins (e.g., Ago1, Ago2, Ago3,Ago4) and their associated miRNAs. See, e.g., Gibbings et al.,Multivesicular bodies associate with components of miRNA effectorcomplexes and modulate miRNA activity, Nat Cell Biol 2009 11:1143-1149.Epub 2009 Aug. 16; Lazzaretti et al., The C-terminal domains of humanTNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently ofArgonaute proteins. RNA. 2009 15:1059-66. Epub 2009 Apr. 21. GW182,which is encoded by the TNRC6A gene (trinucleotide repeat containing6A), functions in post-transcriptional gene silencing through the RNAinterference (RNAi) and microRNA pathways. TNRC6B and TNRC6C are alsomembers of the trinucleotide repeat containing 6 family and play similarroles in gene silencing. GW182 associates with mRNAs and Argonauteproteins in cytoplasmic bodies known as GW-bodies or P-bodies. GW182 isinvolved in miRNA-dependent repression of translation and forsiRNA-dependent endonucleolytic cleavage of complementary mRNAs byargonaute family proteins.

In an aspect, the invention provides a method of characterizing aphenotype comprising analyzing nucleic acid—protein complex biomarkers.As used herein, a nucleic acid—protein complex comprises at least onenucleic acid and at least one protein, and can also include othercomponents such as lipids. A nucleic acid—protein complex can beassociated with a vesicle. In an embodiment, RNA—protein complexes areisolated and the levels of the associated RNAs are assessed, wherein thelevels are used for characterizing the phenotype, e.g., providing adiagnosis, prognosis, theranosis, or other phenotype as describedherein. The RNA can be microRNA. MicroRNAs have been found associatedwith vesicles and proteins. In some cases, this association may serve toprotect miRNAs from degradation via RNAses or other factors. Content ofvarious populations of microRNA can be assessed in a sample, includingwithout limitation vesicle associated miRs, Ago-associated miRs,cell-of-origin vesicle associated miRs, circulating Ago-bound miRs,circulating HDL-bound miRs, and the total miR content.

The protein biomarker used to isolate the complexes can be one or moreArgonaute protein, or other protein that associates with Argonautefamily members. These include without limitation the Argonaute proteinsAgo1, Ago2, Ago3, Ago4, and various isoforms thereof. The proteinbiomarker can be GW182 (TNRC6A), TNRC6B and/or TNRC6C. The proteinbiomarker can be a protein associated with a P-body or a GW-body, suchas SW182, an argonaute, decapping enzyme or RNA helicase. See, e.g.,Kulkami et al. On track with P-bodies. Biochem Soc Trans 2010,38:242-251. The protein biomarker can also be one or more of HNRNPA2B1(Heterogeneous nuclear ribonucleoprotein a2/b1), HNRPAB (Heterogeneousnuclear ribonucleoprotein A/B), ILF2 (Interleukin enhancer bindingfactor 2, 45 kda), NCL (Nucleolin), NPM1 (Nucleophosmin (nucleolarphosphoprotein b23, numatrin)), RPL10A (Ribosomal protein 110a), RPL5(Ribosomal protein 15), RPLP1 (Ribosomal protein, large, p1), RPS12(Ribosomal protein s12), RPS19 (Ribosomal protein s19), SNRPG (Smallnuclear ribonucleoprotein polypeptide g), TROVE2 (Trove domain family,member 2). See Wang et al., Export of microRNAs and microRNA-protectiveprotein by mammalian cells. Nucleic Acids Res. 38:7248-59. Epub 2010Jul. 7. The protein biomarker can also be an apolipoprotein, which areproteins that bind to lipids (oil-soluble substances such as fat andcholesterol) to form lipoproteins, which transport the lipids throughthe lymphatic and circulatory systems. See Vickers et al., MicroRNAs aretransported in plasma and delivered to recipient cells by high-densitylipoproteins, Nat Cell Biol 2011 13:423-33, Epub 2011 Mar. 20. Theapolipoprotein can be apolipoprotein A (including apo A-I, apo A-II, apoA-IV, and apo A-V), apolipoprotein B (including apo B48 and apo B100),apolipoprotein C (including apo C-I, apo C-II, apo C-III, and apo C-IV),apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), or a combination thereof. The apolipoprotein can beapolipoprotein L, including APOL1, APOL2, APOL3, APOL4, APOL5, APOL6,APOLD1, or a combination thereof. Apolipoprotein L (Apo L) belongs tothe high density lipoprotein family that plays a central role incholesterol transport. The protein biomarker can be a component of alipoprotein, such as a component of a chylomicron, very low densitylipoprotein (VLDL), intermediate density lipoprotein (IDL), low densitylipoprotein (LDL) and/or high density lipoprotein (HDL). In anembodiment, the protein biomarker is a component of a LDL or HDL. Thecomponent can be ApoE. The component can be ApoA1. The protein biomarkercan be a general vesicle marker, such as a tetraspanin or other proteinlisted in Table 3, including without limitation CD9, CD63 and/or CD81.The protein biomarker can be a cancer marker such as EpCam, B7H3 and/orCD24. The protein biomarker can be a tissue specific biomarker, such asthe prostate biomarkers PSCA, PCSA and/or PSMA. Combinations of these orother useful protein biomarkers can be used to isolate specificpopulations of complexes of interest.

The nucleic acid—protein complexes can be isolated by using a bindingagent to one or more component of the complexes. Various techniques forisolating proteins are known to those of skill in the art and/orpresented herein, including without limitation affinity isolation,immunocapture, immunoprecipitation, and flow cytometry. The bindingagent can be any appropriate binding agent, including those describedherein such as the one or more binding agent comprises a nucleic acid,DNA molecule, RNA molecule, antibody, antibody fragment, aptamer,peptoid, zDNA, peptide nucleic acid (PNA), locked nucleic acid (LNA),lectin, peptide, dendrimer, membrane protein labeling agent, chemicalcompound, or a combination thereof. In an embodiment, the binding agentcomprises an antibody, antibody conjugate, antibody fragment, and/oraptamer. For additional methods of assessing protein—nucleic acidcomplexes that can be used with the subject invention, see also Wang etal., Export of microRNAs and microRNA-protective protein by mammaliancells. Nucleic Acids Res. 38:7248-59. Epub 2010 Jul. 7; Keene et al.,RIP-Chip: the isolation and identification of mRNAs, microRNAs andprotein components of ribonucleoprotein complexes from cell extracts.Nat Protoc 2006 1:302-07; Hafner, Transcriptome-wide identification ofRNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010141:129-41.

The present invention further provides a method of identifying miRNAsthat are found in complex with proteins. In one embodiment, a populationof protein—nucleic acid complexes is isolated as described above. ThemiRNA content of the population is assessed. This method can be used onvarious samples of interest (e.g., diseased, non-diseased, responder,non-responder) and the miRNA content in the samples can be compared toidentify miRNAs that differentiate between the samples. Methods ofdetecting miRNA are provided herein (arrays, per, etc). The identifiedmiRNAs can be used to characterize a phenotype according to the methodsherein. For example, the samples used for discovery can be cancer andnon-cancer plasma samples. Protein-complexed miRNAs can be identifiedthat distinguish between the cancer and non-cancer samples, and thedistinguishing miRNAs can be assessed in order to detect a cancer in aplasma sample.

The present invention also provides a method of distinguishing microRNApayload within vesicles by removing non-payload miRs from avesicle-containing sample, then assessing the miR content within thevesicles. miRs can be removed from the sample using RNAses or otherentities that degrade miRNA. In some embodiments, the sample is treatedwith an agent to remove microRNAs from protein complexes prior to theRNAse treatment. The agent can be an enzyme that degrades protein, e.g.,a proteinase such as Proteinase K or Trypsin, or any other appropriateenzyme. The method can be used to characterize a phenotype according tothe methods herein by assessing the microRNA fraction contained withvesicles apart from free miRNA or miRNA in circulating proteincomplexes.

Biomarker Detection

A biosignature can be detected qualitatively or quantitatively bydetecting a presence, level or concentration of a circulating biomarker,e.g., a microRNA, protein, vesicle or other biomarker, as disclosedherein. These biosignature components can be detected using a number oftechniques known to those of skill in the art. For example, a biomarkercan be detected by microarray analysis, polymerase chain reaction (PCR)(including PCR-based methods such as real time polymerase chain reaction(RT-PCR), quantitative real time polymerase chain reaction (Q-PCR/qPCR)and the like), hybridization with allele-specific probes, enzymaticmutation detection, ligation chain reaction (LCR), oligonucleotideligation assay (OLA), flow-cytometric heteroduplex analysis, chemicalcleavage of mismatches, mass spectrometry, nucleic acid sequencing,single strand conformation polymorphism (SSCP), denaturing gradient gelelectrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE),restriction fragment polymorphisms, serial analysis of gene expression(SAGE), or combinations thereof. A biomarker, such as a nucleic acid,can be amplified prior to detection. A biomarker can also be detected byimmunoassay, immunoblot, immunoprecipitation, enzyme-linkedimmunosorbent assay (ELISA; EIA), radioimmunoassay (RIA), flowcytometry, or electron microscopy (EM).

Biosignatures can be detected using capture agents and detection agents,as described herein. A capture agent can comprise an antibody, aptameror other entity which recognizes a biomarker and can be used forcapturing the biomarker. Biomarkers that can be captured includecirculating biomarkers, e.g., a protein, nucleic acid, lipid orbiological complex in solution in a bodily fluid. Similarly, the captureagent can be used for capturing a vesicle. A detection agent cancomprise an antibody or other entity which recognizes a biomarker andcan be used for detecting the biomarker vesicle, or which recognizes avesicle and is useful for detecting a vesicle. In some embodiments, thedetection agent is labeled and the label is detected, thereby detectingthe biomarker or vesicle. The detection agent can be a binding agent,e.g., an antibody or aptamer. In other embodiments, the detection agentcomprises a small molecule such as a membrane protein labeling agent.See, e.g., the membrane protein labeling agents disclosed in Alroy etal., U.S. Patent Publication US 2005/0158708. In an embodiment, vesiclesare isolated or captured as described herein, and one or more membraneprotein labeling agent is used to detect the vesicles. In many cases,the antigen or other vesicle-moiety that is recognized by the captureand detection agents are interchangeable. As a non-limiting example,consider a vesicle having a cell-of-origin specific antigen on itssurface and a cancer-specific antigen on its surface. In one instance,the vesicle can be captured using an antibody to the cell-of-originspecific antigen, e.g., by tethering the capture antibody to asubstrate, and then the vesicle is detected using an antibody to thecancer-specific antigen, e.g., by labeling the detection antibody with afluorescent dye and detecting the fluorescent radiation emitted by thedye. In another instance, the vesicle can be captured using an antibodyto the cancer specific antigen, e.g., by tethering the capture antibodyto a substrate, and then the vesicle is detected using an antibody tothe cell-of-origin specific antigen, e.g., by labeling the detectionantibody with a fluorescent dye and detecting the fluorescent radiationemitted by the dye.

In some embodiments, a same biomarker is recognized by both a captureagent and a detection agent. This scheme can be used depending on thesetting. In one embodiment, the biomarker is sufficient to detect avesicle of interest, e.g., to capture cell-of-origin specific vesicles.In other embodiments, the biomarker is multifunctional, e.g., havingboth cell-of-origin specific and cancer specific properties. Thebiomarker can be used in concert with other biomarkers for capture anddetection as well.

One method of detecting a biomarker comprises purifying or isolating aheterogeneous population of vesicles from a biological sample, asdescribed above, and performing a sandwich assay. A vesicle in thepopulation can be captured with a capture agent. The capture agent canbe a capture antibody, such as a primary antibody. The capture antibodycan be bound to a substrate, for example an array, well, or particle.The captured or bound vesicle can be detected with a detection agent,such as a detection antibody. For example, the detection antibody can befor an antigen of the vesicle. The detection antibody can be directlylabeled and detected. Alternatively, the detection agent can beindirectly labeled and detected, such as through an enzyme linkedsecondary antibody that can react with the detection agent. A detectionreagent or detection substrate can be added and the reaction detected,such as described in PCT Publication No. WO2009092386. In anillustrative example wherein the capture agent binds Rab-5b and thedetection agent binds or detects CD63 or caveolin-1, the capture agentcan be an anti-Rab 5b antibody and the detection agent can be ananti-CD63 or anti-caveolin-1 antibody. In some embodiments, the captureagent binds CD9, PSCA, TNFR, CD63, B7H3, MFG-E8, EpCam, Rab, CD81,STEAP, PCSA, PSMA, or 5T4. For example, the capture agent can be anantibody to CD9, PSCA, TNFR, CD63, B7H3, MFG-E8, EpCam, Rab, CD81,STEAP, PCSA, PSMA, or 5T4. The capture agent can also be an antibody toMFG-E8, Annexin V, Tissue Factor, DR3, STEAP, epha2, TMEM211, unc93A,A33, CD24, NGAL, EpCam, MUC17, TROP2, or TETS. The detection agent canbe an agent that binds or detects CD63, CD9, CD81, B7H3, or EpCam, suchas a detection antibody or aptamer to CD63, CD9, CD81, B7H3, or EpCam.Various combinations of capture and/or detection agents can be used inconcert. In an embodiment, the capture agents comprise PCSA, PSMA, B7H3and optionally EpCam, and the detection agents comprise one or moregeneral vesicle biomarker, e.g., a tetraspanin such as CD9, CD63 andCD81. In another embodiment, the capture agents comprise TMEM211 andCD24, and the detection agents comprise one or more tetraspanin such asCD9, CD63 and CD81. In another embodiment, the capture agents compriseCD66 and EpCam, and the detection agents comprise one or moretetraspanin such as CD9, CD63 and CD81. The capture agent and/ordetection agent can be to an antigen comprising one or more of CD9,Erb2, Erb4, CD81, Erb3, MUC16, CD63, DLL4, HLA-Drpe, B7H3, IFNAR, 5T4,PCSA, MICB, PSMA, MFG-E8, Muc1, PSA, Muc2, Unc93a, VEGFR2, EpCAM, VEGFA, TMPRSS2, RAGE*, PSCA, CD40, Muc17, IL-17-RA, and CD80. For example,capture agent and/or detection agent can be to one or more of CD9, CD63,CD81, B7H3, PCSA, MFG-E8, MUC2, EpCam, RAGE and Muc17. Increasingnumbers of such tetraspanins and/or other general vesicle markers canimprove the detection signal in some cases. Proteins or othercirculating biomarkers can also be detected using sandwich approaches.The captured vesicles can be collected and used to analyze the payloadcontained therein, e.g., mRNA, microRNAs, DNA and soluble protein.

In some embodiments, the capture agent binds or targets EpCam, B7H3,RAGE or CD24, and the one or more biomarkers detected on the vesicle areCD9 and/or CD63. In one embodiment, the capture agent binds or targetsEpCam, and the one or more biomarkers detected on the vesicle are CD9,EpCam and/or CD81. The single capture agent can be selected from CD9,PSCA, TNFR, CD63, B7H3, MFG-E8, EpCam, Rab, CD81, STEAP, PCSA, PSMA, or5T4. The single capture agent can also be an antibody to DR3, STEAP,epha2, TMEM211, unc93A, A33, CD24, NGAL, EpCam, MUC17, TROP2, MFG-E8,TF, Annexin V or TETS. In some embodiments, the single capture agent isselected from PCSA, PSMA, B7H3, CD81, CD9 and CD63.

In other embodiments, the capture agent targets PCSA, and the one ormore biomarkers detected on the captured vesicle are B7H3 and/or PSMA.In other embodiments, the capture agent targets PSMA, and the one ormore biomarkers detected on the captured vesicle are B7H3 and/or PCSA.In other embodiments, the capture agent targets B7H3, and the one ormore biomarkers detected on the captured vesicle are PSMA and/or PCSA.In yet other embodiments, the capture agent targets CD63 and the one ormore biomarkers detected on the vesicle are CD81, CD83, CD9 and/or CD63.The different capture agent and biomarker combinations disclosed hereincan be used to characterize a phenotype, such as detecting, diagnosingor prognosing a disease, e.g., a cancer. In some embodiments, vesiclesare analyzed to characterize prostate cancer using a capture agenttargeting EpCam and detection of CD9 and CD63; a capture agent targetingPCSA and detection of B7H3 and PSMA; or a capture agent of CD63 anddetection of CD81. In other embodiments, vesicles are used tocharacterize colon cancer using capture agent targeting CD63 anddetection of CD63, or a capture agent targeting CD9 coupled withdetection of CD63. One of skill will appreciate that targets of captureagents and detection agents can be used interchangeably. In anillustrative example, consider a capture agent targeting PCSA anddetection agents targeting B7H3 and PSMA. Because all of these markersare useful for detecting PCa derived vesicles, B7H3 or PSMA could betargeted by the capture agent and PCSA could be recognized by adetection agent. For example, in some embodiments, the detection agenttargets PCSA, and one or more biomarkers used to capture the vesiclecomprise B7H3 and/or PSMA. In other embodiments, the detection agenttargets PSMA, and the one or more biomarkers used to capture the vesiclecomprise B7H3 and/or PCSA. In other embodiments, the detection agenttargets B7H3, and the one or more biomarkers used to capture the vesiclecomprise PSMA and/or PCSA. In some embodiments, the invention provides amethod of detecting prostate cancer cells in bodily fluid using captureagents and/or detection agents to PSMA, B7H3 and/or PCSA. The bodilyfluid can comprise blood, including serum or plasma. The bodily fluidcan comprise ejaculate or sperm. In further embodiments, the methods ofdetecting prostate cancer further use capture agents and/or detectionagents to CD81, CD83, CD9 and/or CD63. The method further provides amethod of characterizing a GI disorder, comprising capturing vesicleswith one or more of DR3, STEAP, epha2, TMEM211, unc93A, A33, CD24, NGAL,EpCam, MUC17, TROP2, and TETS, and detecting the captured vesicles withone or more general vesicle antigen, such as CD81, CD63 and/or CD9.Additional agents can improve the test performance, e.g., improving testaccuracy or AUC, either by providing additional biologicaldiscriminatory power and/or by reducing experimental noise.

Techniques of detecting biomarkers for use with the invention includethe use of a planar substrate such as an array (e.g., biochip ormicroarray), with molecules immobilized to the substrate as captureagents that facilitate the detection of a particular biosignature. Thearray can be provided as part of a kit for assaying one or morebiomarkers or vesicles. A molecule that identifies the biomarkersdescribed above and shown in FIG. 1 or 3-60 of International PatentApplication Serial No. PCT/US2011/031479, entitled “CirculatingBiomarkers for Disease” and filed Apr. 6, 2011, which application isincorporated by reference in its entirety herein, can be included in anarray for detection and diagnosis of diseases including presymptomaticdiseases. In some embodiments, an array comprises a custom arraycomprising biomolecules selected to specifically identify biomarkers ofinterest. Customized arrays can be modified to detect biomarkers thatincrease statistical performance, e.g., additional biomolecules thatidentifies a biosignature which lead to improved cross-validated errorrates in multivariate prediction models (e.g., logistic regression,discriminant analysis, or regression tree models). In some embodiments,customized array(s) are constructed to study the biology of a disease,condition or syndrome and profile biosignatures in defined physiologicalstates. Markers for inclusion on the customized array be chosen basedupon statistical criteria, e.g., having a desired level of statisticalsignificance in differentiating between phenotypes or physiologicalstates. In some embodiments, standard significance of p-value=0.05 ischosen to exclude or include biomolecules on the microarray. Thep-values can be corrected for multiple comparisons. As an illustrativeexample, nucleic acids extracted from samples from a subject with orwithout a disease can be hybridized to a high density microarray thatbinds to thousands of gene sequences. Nucleic acids whose levels aresignificantly different between the samples with or without the diseasecan be selected as biomarkers to distinguish samples as having thedisease or not. A customized array can be constructed to detect theselected biomarkers. In some embodiments, customized arrays comprise lowdensity microarrays, which refer to arrays with lower number ofaddressable binding agents, e.g., tens or hundreds instead of thousands.Low density arrays can be formed on a substrate. In some embodiments,customizable low density arrays use PCR amplification in plate wells,e.g., TaqMan® Gene Expression Assays (Applied Biosystems by LifeTechnologies Corporation, Carlsbad, Calif.).

A planar array generally contains addressable locations (e.g., pads,addresses, or micro-locations) of biomolecules in an array format. Thesize of the array will depend on the composition and end use of thearray. Arrays can be made containing from 2 different molecules to manythousands. Generally, the array comprises from two to as many as 100,000or more molecules, depending on the end use of the array and the methodof manufacture. A microarray for use with the invention comprises atleast one biomolecule that identifies or captures a biomarker present ina biosignature of interest, e.g., a microRNA or other biomolecule orvesicle that makes up the biosignature. In some arrays, multiplesubstrates are used, either of different or identical compositions.Accordingly, planar arrays may comprise a plurality of smallersubstrates.

The present invention can make use of many types of arrays for detectinga biomarker, e.g., a biomarker associated with a biosignature ofinterest. Useful arrays or microarrays include without limitation DNAmicroarrays, such as cDNA microarrays, oligonucleotide microarrays andSNP microarrays, microRNA arrays, protein microarrays, antibodymicroarrays, tissue microarrays, cellular microarrays (also calledtransfection microarrays), chemical compound microarrays, andcarbohydrate arrays (glycoarrays). These arrays are described in moredetail above. In some embodiments, microarrays comprise biochips thatprovide high-density immobilized arrays of recognition molecules (e.g.,antibodies), where biomarker binding is monitored indirectly (e.g., viafluorescence). FIG. 2A shows an illustrative configuration in whichcapture antibodies against a vesicle antigen of interest are tethered toa surface. The captured vesicles are then detected using detectorantibodies against the same or different vesicle antigens of interest.The capture antibodies can be substituted with tethered aptamers asavailable and desirable. Fluorescent detectors are shown. Otherdetectors can be used similarly, e.g., enzymatic reaction, detectablenanoparticles, radiolabels, and the like. In other embodiments, an arraycomprises a format that involves the capture of proteins by biochemicalor intermolecular interaction, coupled with detection by massspectrometry (MS). The vesicles can be eluted from the surface and thepayload therein, e.g., microRNA, can be analyzed.

An array or microarray that can be used to detect one or more biomarkersof a biosignature can be made according to the methods described in U.S.Pat. Nos. 6,329,209; 6,365,418; 6,406,921; 6,475,808; and 6,475,809, andU.S. patent application Ser. No. 10/884,269, each of which is hereinincorporated by reference in its entirety. Custom arrays to detectspecific selections of sets of biomarkers described herein can be madeusing the methods described in these patents. Commercially availablemicroarrays can also be used to carry out the methods of the invention,including without limitation those from Affymetrix (Santa Clara,Calif.), Illumina (San Diego, Calif.), Agilent (Santa Clara, Calif.),Exiqon (Denmark), or Invitrogen (Carlsbad, Calif.). Custom and/orcommercial arrays include arrays for detection proteins, nucleic acids,and other biological molecules and entities (e.g., cells, vesicles,virii) as described herein.

In some embodiments, molecules to be immobilized on an array compriseproteins or peptides. One or more types of proteins may be immobilizedon a surface. In certain embodiments, the proteins are immobilized usingmethods and materials that minimize the denaturing of the proteins, thatminimize alterations in the activity of the proteins, or that minimizeinteractions between the protein and the surface on which they areimmobilized.

Array surfaces useful may be of any desired shape, form, or size.Non-limiting examples of surfaces include chips, continuous surfaces,curved surfaces, flexible surfaces, films, plates, sheets, or tubes.Surfaces can have areas ranging from approximately a square micron toapproximately 500 cm². The area, length, and width of surfaces may bevaried according to the requirements of the assay to be performed.Considerations may include, for example, ease of handling, limitationsof the material(s) of which the surface is formed, requirements ofdetection systems, requirements of deposition systems (e.g., arrayers),or the like.

In certain embodiments, it is desirable to employ a physical means forseparating groups or arrays of binding islands or immobilizedbiomolecules: such physical separation facilitates exposure of differentgroups or arrays to different solutions of interest. Therefore, incertain embodiments, arrays are situated within microwell plates havingany number of wells. In such embodiments, the bottoms of the wells mayserve as surfaces for the formation of arrays, or arrays may be formedon other surfaces and then placed into wells. In certain embodiments,such as where a surface without wells is used, binding islands may beformed or molecules may be immobilized on a surface and a gasket havingholes spatially arranged so that they correspond to the islands orbiomolecules may be placed on the surface. Such a gasket is preferablyliquid tight. A gasket may be placed on a surface at any time during theprocess of making the array and may be removed if separation of groupsor arrays is no longer necessary.

In some embodiments, the immobilized molecules can bind to one or morebiomarkers or vesicles present in a biological sample contacting theimmobilized molecules. In some embodiments, the immobilized moleculesmodify or are modified by molecules present in the one or more vesiclescontacting the immobilized molecules. Contacting the sample typicallycomprises overlaying the sample upon the array.

Modifications or binding of molecules in solution or immobilized on anarray can be detected using detection techniques known in the art.Examples of such techniques include immunological techniques such ascompetitive binding assays and sandwich assays; fluorescence detectionusing instruments such as confocal scanners, confocal microscopes, orCCD-based systems and techniques such as fluorescence, fluorescencepolarization (FP), fluorescence resonant energy transfer (FRET), totalinternal reflection fluorescence (TIRF), fluorescence correlationspectroscopy (FCS); colorimetric/spectrometric techniques; surfaceplasmon resonance, by which changes in mass of materials adsorbed atsurfaces are measured; techniques using radioisotopes, includingconventional radioisotope binding and scintillation proximity assays(SPA); mass spectroscopy, such as matrix-assisted laserdesorption/ionization mass spectroscopy (MALDI) and MALDI-time of flight(TOF) mass spectroscopy; ellipsometry, which is an optical method ofmeasuring thickness of protein films; quartz crystal microbalance (QCM),a very sensitive method for measuring mass of materials adsorbing tosurfaces; scanning probe microscopies, such as atomic force microscopy(AFM), scanning force microscopy (SFM) or scanning electron microscopy(SEM); and techniques such as electrochemical, impedance, acoustic,microwave, and IR/Raman detection. See, e.g., Mere L, et al.,“Miniaturized FRET assays and microfluidics: key components forultra-high-throughput screening,” Drug Discovery Today 4(8):363-369(1999), and references cited therein; Lakowicz J R, Principles ofFluorescence Spectroscopy, 2nd Edition, Plenum Press (1999), or Jain KK: Integrative Omics, Pharmacoproteomics, and Human Body Fluids. In:Thongboonkerd V, ed., ed. Proteomics of Human Body Fluids: Principles,Methods and Applications. Volume 1: Totowa, N.J.: Humana Press, 2007,each of which is herein incorporated by reference in its entirety.

Microarray technology can be combined with mass spectroscopy (MS)analysis and other tools. Electrospray interface to a mass spectrometercan be integrated with a capillary in a microfluidics device. Forexample, one commercially available system contains eTag reporters thatare fluorescent labels with unique and well-defined electrophoreticmobilities; each label is coupled to biological or chemical probes viacleavable linkages. The distinct mobility address of each eTag reporterallows mixtures of these tags to be rapidly deconvoluted and quantitatedby capillary electrophoresis. This system allows concurrent geneexpression, protein expression, and protein function analyses from thesame sample Jain K K: Integrative Omics, Pharmacoproteomics, and HumanBody Fluids. In: Thongboonkerd V, ed., ed. Proteomics of Human BodyFluids: Principles, Methods and Applications. Volume 1: Totowa, N.J.:Humana Press, 2007, which is herein incorporated by reference in itsentirety.

A biochip can include components for a microfluidic or nanofluidicassay. A microfluidic device can be used for isolating or analyzingbiomarkers, such as determining a biosignature. Microfluidic systemsallow for the miniaturization and compartmentalization of one or moreprocesses for isolating, capturing or detecting a vesicle, detecting amicroRNA, detecting a circulating biomarker, detecting a biosignature,and other processes. The microfluidic devices can use one or moredetection reagents in at least one aspect of the system, and such adetection reagent can be used to detect one or more biomarkers. In oneembodiment, the device detects a biomarker on an isolated or boundvesicle. Various probes, antibodies, proteins, or other binding agentscan be used to detect a biomarker within the microfluidic system. Thedetection agents may be immobilized in different compartments of themicrofluidic device or be entered into a hybridization or detectionreaction through various channels of the device.

A vesicle in a microfluidic device can be lysed and its contentsdetected within the microfluidic device, such as proteins or nucleicacids, e.g., DNA or RNA such as miRNA or mRNA. The nucleic acid may beamplified prior to detection, or directly detected, within themicrofluidic device. Thus microfluidic system can also be used formultiplexing detection of various biomarkers. In an embodiment, vesiclesare captured within the microfluidic device, the captured vesicles arelysed, and a biosignature of microRNA from the vesicle payload isdetermined. The biosignature can further comprise the capture agent usedto capture the vesicle.

Novel nanofabrication techniques are opening up the possibilities forbiosensing applications that rely on fabrication of high-density,precision arrays, e.g., nucleotide-based chips and protein arraysotherwise know as heterogeneous nanoarrays. Nanofluidics allows afurther reduction in the quantity of fluid analyte in a microchip tonanoliter levels, and the chips used here are referred to as nanochips.(See, e.g., Unger M et al., Biotechniques 1999; 27(5):1008-14, KartalovE P et al., Biotechniques 2006; 40(1):85-90, each of which are hereinincorporated by reference in their entireties.) Commercially availablenanochips currently provide simple one step assays such as totalcholesterol, total protein or glucose assays that can be run bycombining sample and reagents, mixing and monitoring of the reaction.Gel-free analytical approaches based on liquid chromatography (LC) andnanoLC separations (Cutillas et al. Proteomics, 2005; 5:101-112 andCutillas et al., Mol Cell Proteomics 2005; 4:1038-1051, each of which isherein incorporated by reference in its entirety) can be used incombination with the nanochips.

An array suitable for identifying a disease, condition, syndrome orphysiological status can be included in a kit. A kit can include, asnon-limiting examples, one or more reagents useful for preparingmolecules for immobilization onto binding islands or areas of an array,reagents useful for detecting binding of a vesicle to immobilizedmolecules, and instructions for use.

Further provided herein is a rapid detection device that facilitates thedetection of a particular biosignature in a biological sample. Thedevice can integrate biological sample preparation with polymerase chainreaction (PCR) on a chip. The device can facilitate the detection of aparticular biosignature of a vesicle in a biological sample, and anexample is provided as described in Pipper et al., Angewandte Chemie,47(21), p. 3900-3904 (2008), which is herein incorporated by referencein its entirety. A biosignature can be incorporated usingmicro-/nano-electrochemical system (MEMS/NEMS) sensors and oral fluidfor diagnostic applications as described in Li et al., Adv Dent Res18(1): 3-5 (2005), which is herein incorporated by reference in itsentirety.

As an alternative to planar arrays, assays using particles, such as beadbased assays as described herein, can be used in combination with flowcytometry. Multiparametric assays or other high throughput detectionassays using bead coatings with cognate ligands and reporter moleculeswith specific activities consistent with high sensitivity automation canbe used. In a bead based assay system, a binding agent for a biomarkeror vesicle, such as a capture agent (e.g. capture antibody), can beimmobilized on an addressable microsphere. Each binding agent for eachindividual binding assay can be coupled to a distinct type ofmicrosphere (i.e., microbead) and the assay reaction takes place on thesurface of the microsphere, such as depicted in FIG. 2B. A binding agentfor a vesicle can be a capture antibody coupled to a bead. Dyedmicrospheres with discrete fluorescence intensities are loadedseparately with their appropriate binding agent or capture probes. Thedifferent bead sets carrying different binding agents can be pooled asnecessary to generate custom bead arrays. Bead arrays are then incubatedwith the sample in a single reaction vessel to perform the assay.Examples of microfluidic devices that may be used, or adapted for usewith the invention, include but are not limited to those describedherein.

Product formation of the biomarker with an immobilized capture moleculeor binding agent can be detected with a fluorescence based reportersystem (see for example, FIG. 2A-B). The biomarker can either be labeleddirectly by a fluorophore or detected by a second fluorescently labeledcapture biomolecule. The signal intensities derived from capturedbiomarkers can be measured in a flow cytometer. The flow cytometer canfirst identify each microsphere by its individual color code. Forexample, distinct beads can be dyed with discrete fluorescenceintensities such that each bead with a different intensity has adifferent binding agent. The beads can be labeled or dyed with at least2 different labels or dyes. In some embodiments, the beads are labeledwith at least 3, 4, 5, 6, 7, 8, 9, or 10 different labels. The beadswith more than one label or dye can also have various ratios andcombinations of the labels or dyes. The beads can be labeled or dyedexternally or may have intrinsic fluorescence or signaling labels.

The amount of captured biomarkers on each individual bead can bemeasured by the second color fluorescence specific for the bound target.This allows multiplexed quantitation of multiple targets from a singlesample within the same experiment. Sensitivity, reliability and accuracyare compared or can be improved to standard microtiter ELISA procedures.An advantage of a bead-based system is the individual coupling of thecapture biomolecule or binding agent for a vesicle to distinctmicrospheres provides multiplexing capabilities. For example, asdepicted in FIG. 2C, a combination of 5 different biomarkers to bedetected (detected by antibodies to antigens such as CD63, CD9, CD81,B7H3, and EpCam) and 20 biomarkers for which to capture a vesicle,(using capture antibodies, such as antibodies to CD9, PSCA, TNFR, CD63,B7H3, MFG-E8, EpCam, Rab, CD81, STEAP, PCSA, PSMA, 5T4, and/or CD24) canresult in approximately 100 combinations to be detected. As shown inFIG. 2C as “EpCam 2x,” “CD63 2X,” multiple antibodies to a single targetcan be used to probe detection against various epitopes. In anotherexample, multiplex analysis comprises capturing a vesicle using abinding agent to CD24 and detecting the captured vesicle using a bindingagent for CD9, CD63, and/or CD81. The captured vesicles can be detectedusing a detection agent such as an antibody. The detection agents can belabeled directly or indirectly, as described herein.

Multiplexing of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 25, 50, 75 or 100 different biomarkers may beperformed. For example, an assay of a heterogeneous population ofvesicles can be performed with a plurality of particles that aredifferentially labeled. There can be at least 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 75 or 100differentially labeled particles. The particles may be externallylabeled, such as with a tag, or they may be intrinsically labeled. Eachdifferentially labeled particle can be coupled to a capture agent, suchas a binding agent, for a vesicle, resulting in capture of a vesicle.The multiple capture agents can be selected to characterize a phenotypeof interest, including capture agents against general vesiclebiomarkers, cell-of-origin specific biomarkers, and disease biomarkers.One or more biomarkers of the captured vesicle can then be detected by aplurality of binding agents. The binding agent can be directly labeledto facilitate detection. Alternatively, the binding agent is labeled bya secondary agent. For example, the binding agent may be an antibody fora biomarker on the vesicle. The binding agent is linked to biotin. Asecondary agent comprises streptavidin linked to a reporter and can beadded to detect the biomarker. In some embodiments, the captured vesicleis assayed for at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 25, 50, 75 or 100 different biomarkers. For example,multiple detectors, i.e., detection of multiple biomarkers of a capturedvesicle or population of vesicles, can increase the signal obtained,permitted increased sensitivity, specificity, or both, and the use ofsmaller amounts of samples. For example, detection with more than onegeneral vesicle marker can improve the signal as compared to using alesser number of detection markers, such as a single marker. Toillustrate, detection of vesicles with labeled binding agents to two orthree of CD9, CD63 and CD81 can improve the signal compared to detectionwith any one of the tetraspanins individually.

An immunoassay based method or sandwich assay can also be used to detecta biomarker of a vesicle. An example includes ELISA. A binding agent orcapture agent can be bound to a well. For example an antibody to anantigen of a vesicle can be attached to a well. A biomarker on thecaptured vesicle can be detected based on the methods described herein.FIG. 2A shows an illustrative schematic for a sandwich-type ofimmunoassay. The capture antibody can be against a vesicle antigen ofinterest, e.g., a general vesicle biomarker, a cell-of-origin marker, ora disease marker. In the figure, the captured vesicles are detectedusing fluorescently labeled antibodies against vesicle antigens ofinterest. Multiple capture antibodies can be used, e.g., indistinguishable addresses on an array or different wells of animmunoassay plate. The detection antibodies can be against the sameantigen as the capture antibody, or can be directed against othermarkers. The capture antibodies can be substituted with alternatebinding agents, such as tethered aptamers or lectins, and/or thedetector antibodies can be similarly substituted, e.g., with detectable(e.g., labeled) aptamers, lectins or other binding proteins or entities.In an embodiment, one or more capture agents to a general vesiclebiomarker, a cell-of-origin marker, and/or a disease marker are usedalong with detection agents against general vesicle biomarker, such astetraspanin molecules including without limitation one or more of CD9,CD63 and CD81.

FIG. 2D presents an illustrative schematic for analyzing vesiclesaccording to the methods of the invention. Capture agents are used tocapture vesicles, detectors are used to detect the captured vesicles,and the level or presence of the captured and detected antibodies isused to characterize a phenotype. Capture agents, detectors andcharacterizing phenotypes can be any of those described herein. Forexample, capture agents include antibodies or aptamers tethered to asubstrate that recognize a vesicle antigen of interest, detectorsinclude labeled antibodies or aptamers to a vesicle antigen of interest,and characterizing a phenotype includes a diagnosis, prognosis, ortheranosis of a disease. In the scheme shown in FIG. 2D i), a populationof vesicles is captured with one or more capture agents against generalvesicle biomarkers (6300). The captured vesicles are then labeled withdetectors against cell-of-origin biomarkers (6301) and/or diseasespecific biomarkers (6302). If only cell-of-origin detectors are used(6301), the biosignature used to characterize the phenotype (6303) caninclude the general vesicle markers (6300) and the cell-of-originbiomarkers (6301). If only disease detectors are used (6302), thebiosignature used to characterize the phenotype (6303) can include thegeneral vesicle markers (6300) and the disease biomarkers (6302).Alternately, detectors are used to detect both cell-of-origin biomarkers(6301) and disease specific biomarkers (6302). In this case, thebiosignature used to characterize the phenotype (6303) can include thegeneral vesicle markers (6300), the cell-of-origin biomarkers (6301) andthe disease biomarkers (6302). The biomarkers combinations are selectedto characterize the phenotype of interest and can be selected from thebiomarkers and phenotypes described herein.

In the scheme shown in FIG. 2D ii), a population of vesicles is capturedwith one or more capture agents against cell-of-origin biomarkers (6310)and/or disease biomarkers (6311). The captured vesicles are thendetected using detectors against general vesicle biomarkers (6312). Ifonly cell-of-origin capture agents are used (6310), the biosignatureused to characterize the phenotype (6313) can include the cell-of-originbiomarkers (6310) and the general vesicle markers (6312). If onlydisease biomarker capture agents are used (6311), the biosignature usedto characterize the phenotype (6313) can include the disease biomarkers(6311) and the general vesicle biomarkers (6312). Alternately, captureagents to one or more cell-of-origin biomarkers (6310) and one or moredisease specific biomarkers (6311) are used to capture vesicles. In thiscase, the biosignature used to characterize the phenotype (6313) caninclude the cell-of-origin biomarkers (6310), the disease biomarkers(6311), and the general vesicle markers (6313). The biomarkerscombinations are selected to characterize the phenotype of interest andcan be selected from the biomarkers and phenotypes described herein.

Biomarkers comprising vesicle payload can be analyzed to characterize aphenotype. Payload comprises the biological entities contained within avesicle membrane. These entities include without limitation nucleicacids, e.g., mRNA, microRNA, or DNA fragments; protein, e.g., solubleand membrane associated proteins; carbohydrates; lipids; metabolites;and various small molecules, e.g., hormones. The payload can be part ofthe cellular milieu that is encapsulated as a vesicle is formed in thecellular environment. In some embodiments of the invention, the payloadis analyzed in addition to detecting vesicle surface antigens. Specificpopulations of vesicles can be captured as described above then thepayload in the captured vesicles can be used to characterize aphenotype. For example, vesicles captured on a substrate can be furtherisolated to assess the payload therein. Alternately, the vesicles in asample are detected and sorted without capture. The vesicles so detectedcan be further isolated to assess the payload therein. In an embodiment,vesicle populations are sorted by flow cytometry and the payload in thesorted vesicles is analyzed. In the scheme shown in FIG. 2E iii), apopulation of vesicles is captured and/or detected (6320) using one ormore of cell-of-origin biomarkers (6320), disease biomarkers (6321), andgeneral vesicle markers (6322). The vesicles can also be detected usingone or more of angiogenic or immunomodulatory biomarkers. The payload ofthe isolated vesicles is assessed (6323). A biosignature detected withinthe payload can be used to characterize a phenotype (6324). In anon-limiting example, a vesicle population can be analyzed in a plasmasample from a patient using antibodies against one or more vesicleantigens of interest. The antibodies can be capture antibodies which aretethered to a substrate to isolate a desired vesicle population.Alternately, the antibodies can be directly labeled and the labeledvesicles isolated by sorting with flow cytometry. The presence or levelof microRNA or mRNA extracted from the isolated vesicle population canbe used to detect a biosignature. The biosignature is then used todiagnose, prognose or theranose the patient.

In other embodiments, vesicle payload is analyzed in a vesiclepopulation without first capturing or detected subpopulations ofvesicles. For example, vesicles can be generally isolated from a sampleusing centrifugation, filtration, chromatography, or other techniques asdescribed herein. The payload of the isolated vesicles can be analyzedthereafter to detect a biosignature and characterize a phenotype. In thescheme shown in FIG. 2E iv), a population of vesicles is isolated (6330)and the payload of the isolated vesicles is assessed (6331). Abiosignature detected within the payload can be used to characterize aphenotype (6332). In a non-limiting example, a vesicle population isisolated from a plasma sample from a patient using size exclusion andmembrane filtration. The presence or level of microRNA or mRNA extractedfrom the vesicle population is used to detect a biosignature. Thebiosignature is then used to diagnose, prognose or theranose thepatient.

The methods of characterizing a phenotype can employ a combination oftechniques to assess a vesicle population in a sample of interest. In anembodiment, the sample is split into various aliquots and each isanalyzed separately. For example, protein content of one or more aliquotis determined and microRNA content of one or more other aliquot isdetermined. The protein content and microRNA content can be combined tocharacterize a phenotype. In another embodiment, vesicles of interestare isolated and the payload therein is assessed. For example, apopulation of vesicles with a given surface marker can be isolated byaffinity isolation such as flow cytometry immunoprecipitation, or otherimmunocapture technique using a binding agent to the surface marker ofinterest. The isolated vesicles can then be assessed for biomarkers suchas surface content or payload. The biomarker profile of vesicles havingthe given surface marker can be used to characterize a phenotype. As anon-limiting example, a PCSA+ capture agent can be used to isolate aprostate specific vesicle population. Levels of surface antigens such asPCSA itself, PSMA, B7H3, or EpCam can be assessed from the PCSA+vesicles. Levels of payload in the PCSA+ can also be assessed, e.g.,microRNA or mRNA content. A biosignature can be constructed from acombination of the markers in the PCSA+ vesicle population.

A peptide or protein biomarker can be analyzed by mass spectrometry orflow cytometry. Proteomic analysis of a vesicle may be carried out byimmunocytochemical staining, Western blotting, electrophoresis,SDS-PAGE, chromatography, x-ray crystallography or other proteinanalysis techniques in accordance with procedures well known in the art.In other embodiments, the protein biosignature of a vesicle may beanalyzed using 2 D differential gel electrophoresis as described in,Chromy et al. J Proteome Res, 2004; 3:1120-1127, which is hereinincorporated by reference in its entirety, or with liquid chromatographymass spectrometry as described in Zhang et al. Mol Cell Proteomics,2005; 4:144-155, which is herein incorporated by reference in itsentirety. A vesicle may be subjected to activity-based protein profilingdescribed for example, in Berger et al., Am J Pharmacogenomics, 2004;4:371-381, which is in incorporated by reference in its entirety. Inother embodiments, a vesicle may be profiled using nanospray liquidchromatography-tandem mass spectrometry as described in Pisitkun et al.,Proc Natl Acad Sci USA, 2004; 101:13368-13373, which is hereinincorporated by reference in its entirety. In another embodiment, thevesicle may be profiled using tandem mass spectrometry (MS) such asliquid chromatography/MS/MS (LC-MS/MS) using for example a LTQ andLTQ-FT ion trap mass spectrometer. Protein identification can bedetermined and relative quantitation can be assessed by comparingspectral counts as described in Smalley et al., J Proteome Res, 2008;7:2088-2096, which is herein incorporated by reference in its entirety.

The expression of circulating protein biomarkers or protein payloadwithin a vesicle can also be identified. The latter analysis canoptionally follow the isolation of specific vesicles using captureagents to capture populations of interest. In an embodiment,immunocytochemical staining is used to analyze protein expression. Thesample can be resuspended in buffer, centrifuged at 100×g for example,for 3 minutes using a cytocentrifuge on adhesive slides in preparationfor immunocytochemical staining. The cytospins can be air-driedovernight and stored at −80° C. until staining. Slides can then be fixedand blocked with serum-free blocking reagent. The slides can then beincubated with a specific antibody to detect the expression of a proteinof interest. In some embodiments, the vesicles are not purified,isolated or concentrated prior to protein expression analysis.

Biosignatures comprising vesicle payload can be characterized byanalysis of a metabolite marker or metabolite within the vesicle.Various metabolite-oriented approaches have been described such asmetabolite target analyses, metabolite profiling, or metabolicfingerprinting, see for example, Denkert et al., Molecular Cancer 2008;7: 4598-4617, Ellis et al., Analyst 2006; 8: 875-885, Kuhn et al.,Clinical Cancer Research 2007; 24: 7401-7406, Fiehn O., Comp FunctGenomics 2001; 2:155-168, Fancy et al., Rapid Commun Mass Spectrom20(15): 2271-80 (2006), Lindon et al., Pharm Res, 23(6): 1075-88 (2006),Holmes et al., Anal Chem. 2007 Apr. 1; 79(7):2629-40. Epub 2007 Feb. 27.Erratum in: Anal Chem. 2008 Aug. 1; 80(15):6142-3, Stanley et al., AnalBiochem. 2005 Aug. 15; 343(2): 195-202., Lehtimäki et al., J Biol Chem.2003 Nov. 14; 278(46):45915-23, each of which is herein incorporated byreference in its entirety.

Peptides can be analyzed by systems described in Jain K K: IntegrativeOmics, Pharmacoproteomics, and Human Body Fluids. In: Thongboonkerd V,ed., ed. Proteomics of Human Body Fluids: Principles, Methods andApplications. Volume 1: Totowa, N.J.: Humana Press, 2007, which isherein incorporated by reference in its entirety. This system cangenerate sensitive molecular fingerprints of proteins present in a bodyfluid as well as in vesicles. Commercial applications which include theuse of chromatography/mass spectroscopy and reference libraries of allstable metabolites in the human body, for example Paradigm Genetic'sHuman Metabolome Project, may be used to determine a metabolitebiosignature. Other methods for analyzing a metabolic profile caninclude methods and devices described in U.S. Pat. No. 6,683,455(Metabometrix), U.S. Patent Application Publication Nos. 20070003965 and20070004044 (Biocrates Life Science), each of which is hereinincorporated by reference in its entirety. Other proteomic profilingtechniques are described in Kennedy, Toxicol Lett 120:379-384 (2001),Berven et al., Curr Pharm Biotechnol 7(3): 147-58 (2006), Conrads etal., Expert Rev Proteomics 2(5): 693-703, Decramer et al., World J Urol25(5): 457-65 (2007), Decramer et al., Mol Cell Proteomics 7(10):1850-62 (2008), Decramer et al., Contrib Nephrol, 160: 127-41 (2008),Diamandis, J Proteome Res 5(9): 2079-82 (2006), Immler et al.,Proteomics 6(10): 2947-58 (2006), Khan et al., J Proteome Res 5(10):2824-38 (2006), Kumar et al., Biomarkers 11(5): 385-405 (2006), Noble etal., Breast Cancer Res Treat 104(2): 191-6 (2007), Omenn, Dis Markers20(3): 131-4 (2004), Powell et al., Expert Rev Proteomics 3(1): 63-74(2006), Rai et al., Arch Pathol Lab Med, 126(12): 1518-26 (2002),Ramstrom et al., Proteomics, 3(2): 184-90 (2003), Tammen et al., BreastCancer Res Treat, 79(1): 83-93 (2003), Theodorescu et al., Lancet Oncol,7(3): 230-40 (2006), or Zurbig et al., Electrophoresis, 27(11): 2111-25(2006).

For analysis of mRNAs, miRNAs or other small RNAs, the total RNA can beisolated using any known methods for isolating nucleic acids such asmethods described in U.S. Patent Application Publication No. 2008132694,which is herein incorporated by reference in its entirety. Theseinclude, but are not limited to, kits for performing membrane based RNApurification, which are commercially available. Generally, kits areavailable for the small-scale (30 mg or less) preparation of RNA fromcells and tissues, for the medium scale (250 mg tissue) preparation ofRNA from cells and tissues, and for the large scale (1 g maximum)preparation of RNA from cells and tissues. Other commercially availablekits for effective isolation of small RNA-containing total RNA areavailable. Such methods can be used to isolate nucleic acids fromvesicles.

Alternatively, RNA can be isolated using the method described in U.S.Pat. No. 7,267,950, which is herein incorporated by reference in itsentirety. U.S. Pat. No. 7,267,950 describes a method of extracting RNAfrom biological systems (cells, cell fragments, organelles, tissues,organs, or organisms) in which a solution containing RNA is contactedwith a substrate to which RNA can bind and RNA is withdrawn from thesubstrate by applying negative pressure. Alternatively, RNA may beisolated using the method described in U.S. Patent Application No.20050059024, which is herein incorporated by reference in its entirety,which describes the isolation of small RNA molecules. Other methods aredescribed in U.S. Patent Application No. 20050208510, 20050277121,20070238118, each of which is incorporated by reference in its entirety.

In one embodiment, mRNA expression analysis can be carried out on mRNAsfrom a vesicle isolated from a sample. In some embodiments, the vesicleis a cell-of-origin specific vesicle. An expression pattern generatedfrom a vesicle can be indicative of a given disease state, diseasestage, therapy related signature, or physiological condition.

In one embodiment, once the total RNA has been isolated, cDNA can besynthesized and either qRT-PCR assays (e.g. Applied Biosystem's Taqman®assays) for specific mRNA targets can be performed according tomanufacturer's protocol, or an expression microarray can be performed tolook at highly multiplexed sets of expression markers in one experiment.Methods for establishing gene expression profiles include determiningthe amount of RNA that is produced by a gene that can code for a proteinor peptide. This can be accomplished by quantitative reversetranscriptase PCR (qRT-PCR), competitive RT-PCR, real time RT-PCR,differential display RT-PCR, Northern Blot analysis or other relatedtests. While it is possible to conduct these techniques using individualPCR reactions, it is also possible to amplify complementary DNA (cDNA)or complementary RNA (cRNA) produced from mRNA and analyze it viamicroarray.

The level of a miRNA product in a sample can be measured using anyappropriate technique that is suitable for detecting mRNA expressionlevels in a biological sample, including but not limited to Northernblot analysis, RT-PCR, qRT-PCR, in situ hybridization or microarrayanalysis. For example, using gene specific primers and target cDNA,qRT-PCR enables sensitive and quantitative miRNA measurements of eithera small number of target miRNAs (via singleplex and multiplex analysis)or the platform can be adopted to conduct high throughput measurementsusing 96-well or 384-well plate formats. See for example, Ross J S etal, Oncologist. 2008 May; 13(5):477-93, which is herein incorporated byreference in its entirety. A number of different array configurationsand methods for microarray production are known to those of skill in theart and are described in U.S. patents such as: U.S. Pat. No. 5,445,934;5,532,128; 5,556,752; 5,242,974; 5,384,261; 5,405,783; 5,412,087;5,424,186; 5,429,807; 5,436,327; 5,472,672; 5,527,681; 5,529,756;5,545,531; 5,554,501; 5,561,071; 5,571,639; 5,593,839; 5,599,695;5,624,711; 5,658,734; or 5,700,637; each of which is herein incorporatedby reference in its entirety. Other methods of profiling miRNAs aredescribed in Taylor et al., Gynecol Oncol. 2008 July; 110(1): 13-21,Gilad et al, PLoS ONE. 2008 Sep. 5; 3(9):e3148, Lee et al., Annu RevPathol. 2008 Sep. 25 and Mitchell et al, Proc Natl Acad Sci USA. 2008Jul. 29; 105(30):10513-8, Shen R et al, BMC Genomics. 2004 Dec. 14;5(1):94, Mina L et al, Breast Cancer Res Treat. 2007 June;103(2):197-208, Zhang L et al, Proc Natl Acad Sci USA. 2008 May 13;105(19):7004-9, Ross J S et al, Oncologist. 2008 May; 13(5):477-93,Schetter A J et al, JAMA. 2008 Jan. 30; 299(4):425-36, Staudt L M, NEngl J Med 2003; 348:1777-85, Mulligan G et al, Blood. 2007 Apr. 15;109(8):3177-88. Epub 2006 Dec. 21, McLendon R et al, Nature. 2008 Oct.23; 455(7216):1061-8, and U.S. Pat. Nos. 5,538,848, 5,723,591,5,876,930, 6,030,787, 6,258,569, and 5,804,375, each of which is hereinincorporated by reference. In some embodiments, arrays of microRNApanels are use to simultaneously query the expression of multiple miRs.The Exiqon mIRCURY LNA microRNA PCR system panel (Exiqon, Inc., Woburn,Mass.) or the TaqMan® MicroRNA Assays and Arrays systems from AppliedBiosystems (Foster City, Calif.) can be used for such purposes.

Microarray technology allows for the measurement of the steady-statemRNA or miRNA levels of thousands of transcripts or miRNAssimultaneously thereby presenting a powerful tool for identifyingeffects such as the onset, arrest, or modulation of uncontrolled cellproliferation. Two microarray technologies, such as cDNA arrays andoligonucleotide arrays can be used. The product of these analyses aretypically measurements of the intensity of the signal received from alabeled probe used to detect a cDNA sequence from the sample thathybridizes to a nucleic acid sequence at a known location on themicroarray. Typically, the intensity of the signal is proportional tothe quantity of cDNA, and thus mRNA or miRNA, expressed in the samplecells. A large number of such techniques are available and useful.Methods for determining gene expression can be found in U.S. Pat. No.6,271,002 to Linsley, et al.; U.S. Pat. No. 6,218,122 to Friend, et al.;U.S. Pat. No. 6,218,114 to Peck et al.; or U.S. Pat. No. 6,004,755 toWang, et al., each of which is herein incorporated by reference in itsentirety.

Analysis of an expression level can be conducted by comparing suchintensities. This can be performed by generating a ratio matrix of theexpression intensities of genes in a test sample versus those in acontrol sample. The control sample may be used as a reference, anddifferent references to account for age, ethnicity and sex may be used.Different references can be used for different conditions or diseases,as well as different stages of diseases or conditions, as well as fordetermining therapeutic efficacy.

For instance, the gene expression intensities of mRNA or miRNAs derivedfrom a diseased tissue, including those isolated from vesicles, can becompared with the expression intensities of the same entities in normaltissue of the same type (e.g., diseased breast tissue sample versusnormal breast tissue sample). A ratio of these expression intensitiesindicates the fold-change in gene expression between the test andcontrol samples. Alternatively, if vesicles are not normally present infrom normal tissues (e.g. breast) then absolute quantitation methods, asis known in the art, can be used to define the number of miRNA moleculespresent without the requirement of miRNA or mRNA isolated from vesiclesderived from normal tissue.

Gene expression profiles can also be displayed in a number of ways. Acommon method is to arrange raw fluorescence intensities or ratio matrixinto a graphical dendogram where columns indicate test samples and rowsindicate genes. The data is arranged so genes that have similarexpression profiles are proximal to each other. The expression ratio foreach gene is visualized as a color. For example, a ratio less than one(indicating down-regulation) may appear in the blue portion of thespectrum while a ratio greater than one (indicating up-regulation) mayappear as a color in the red portion of the spectrum. Commerciallyavailable computer software programs are available to display such data.

mRNAs or miRNAs that are considered differentially expressed can beeither over expressed or under expressed in patients with a diseaserelative to disease free individuals. Over and under expression arerelative terms meaning that a detectable difference (beyond thecontribution of noise in the system used to measure it) is found in theamount of expression of the mRNAs or miRNAs relative to some baseline.In this case, the baseline is the measured mRNA/miRNA expression of anon-diseased individual. The mRNA/miRNA of interest in the diseasedcells can then be either over or under expressed relative to thebaseline level using the same measurement method. Diseased, in thiscontext, refers to an alteration of the state of a body that interruptsor disturbs, or has the potential to disturb, proper performance ofbodily functions as occurs with the uncontrolled proliferation of cells.Someone is diagnosed with a disease when some aspect of that person'sgenotype or phenotype is consistent with the presence of the disease.However, the act of conducting a diagnosis or prognosis includes thedetermination of disease/status issues such as determining thelikelihood of relapse or metastasis and therapy monitoring. In therapymonitoring, clinical judgments are made regarding the effect of a givencourse of therapy by comparing the expression of genes over time todetermine whether the mRNA/miRNA expression profiles have changed or arechanging to patterns more consistent with normal tissue.

Levels of over and under expression are distinguished based on foldchanges of the intensity measurements of hybridized microarray probes. A2× difference is preferred for making such distinctions or a p-valueless than 0.05. That is, before an mRNA/miRNA is the to bedifferentially expressed in diseased/relapsing versusnormal/non-relapsing cells, the diseased cell is found to yield at least2 times more, or 2 times less intensity than the normal cells. Thegreater the fold difference, the more preferred is use of the gene as adiagnostic or prognostic tool. mRNA/miRNAs selected for the expressionprofiles of the instant invention have expression levels that result inthe generation of a signal that is distinguishable from those of thenormal or non-modulated genes by an amount that exceeds background usingclinical laboratory instrumentation.

Statistical values can be used to confidently distinguish modulated fromnon-modulated mRNA/miRNA and noise. Statistical tests find themRNA/miRNA most significantly different between diverse groups ofsamples. The Student's t-test is an example of a robust statistical testthat can be used to find significant differences between two groups. Thelower the p-value, the more compelling the evidence that the gene showsa difference between the different groups. Nevertheless, sincemicroarrays measure more than one mRNA/miRNA at a time, tens ofthousands of statistical tests may be performed at one time. Because ofthis, one is unlikely to see small p-values just by chance andadjustments for this using a Sidak correction as well as arandomization/permutation experiment can be made. A p-value less than0.05 by the t-test is evidence that the gene is significantly different.More compelling evidence is a p-value less then 0.05 after the Sidakcorrection is factored in. For a large number of samples in each group,a p-value less than 0.05 after the randomization/permutation test is themost compelling evidence of a significant difference.

In one embodiment, a method of generating a posterior probability scoreto enable diagnostic, prognostic, therapy-related, or physiologicalstate specific biosignature scores can be arrived at by obtainingcirculating biomarker expression data from a statistically significantnumber of patients; applying linear discrimination analysis to the datato obtain selected biomarkers; and applying weighted expression levelsto the selected biomarkers with discriminate function factor to obtain aprediction model that can be applied as a posterior probability score.Other analytical tools can also be used to answer the same question suchas, logistic regression and neural network approaches.

For instance, the following can be used for linear discriminantanalysis:

where,

-   -   I(p_(s)i_(d))=The log base 2 intensity of the probe set enclosed        in parenthesis. d(cp)=The discriminant function for the disease        positive class d(C_(N))=The discriminant function for the        disease negative class    -   P(_(CP))=The posterior p-value for the disease positive class    -   P(_(CN))=The posterior p-value for the disease negative class

Numerous other well-known methods of pattern recognition are available.The following references provide some examples: Weighted Voting: Golubet al. (1999); Support Vector Machines: Su et al. (2001); and Ramaswamyet al. (2001); K-nearest Neighbors: Ramaswamy (2001); and CorrelationCoefficients: van't Veer et al. (2002), all of which are hereinincorporated by reference in their entireties.

A biosignature portfolio, further described below, can be establishedsuch that the combination of biomarkers in the portfolio exhibitimproved sensitivity and specificity relative to individual biomarkersor randomly selected combinations of biomarkers. In one embodiment, thesensitivity of the biosignature portfolio can be reflected in the folddifferences, for example, exhibited by a transcript's expression in thediseased state relative to the normal state. Specificity can bereflected in statistical measurements of the correlation of thesignaling of transcript expression with the condition of interest. Forexample, standard deviation can be a used as such a measurement. Inconsidering a group of biomarkers for inclusion in a biosignatureportfolio, a small standard deviation in expression measurementscorrelates with greater specificity. Other measurements of variationsuch as correlation coefficients can also be used in this capacity.

Another parameter that can be used to select mRNA/miRNA that generate asignal that is greater than that of the non-modulated mRNA/miRNA ornoise is the use of a measurement of absolute signal difference. Thesignal generated by the modulated mRNA/miRNA expression is at least 20%different than those of the normal or non-modulated gene (on an absolutebasis). It is even more preferred that such mRNA/miRNA produceexpression patterns that are at least 30% different than those of normalor non-modulated mRNA/miRNA.

MiRNA can also be detected and measured by amplification from abiological sample and measured using methods described in U.S. Pat. No.7,250,496, U.S. Application Publication Nos. 20070292878, 20070042380 or20050222399 and references cited therein, each of which is hereinincorporated by reference in its entirety. The microRNA can be assessedas in U.S. Pat. No. 7,888,035, entitled “METHODS FOR ASSESSING RNAPATTERNS,” issued Feb. 15, 2011, which application is incorporated byreference herein in its entirety.

The levels of microRNA can be normalized using various techniques knownto those of skill in the art. For example, relative quantification ofmiRNA expression can be performed using the 2^(−ΔΔCT) method (AppliedBiosystems User Bulletin No 2). The levels of microRNA can also benormalized to housekeeping nucleic acids, such as housekeeping mRNAs,microRNA or snoRNA. Further methods for normalizing miRNA levels thatcan be used with the invention are described further in Vasilescu,MicroRNA fingerprints identify miR-150 as a plasma prognostic marker inpatients with sepsis. PLoS One. 2009 Oct. 12; 4(10):e7405; and Peltierand Latham, Normalization of microRNA expression levels in quantitativeRT-PCR assays: identification of suitable reference RNA targets innormal and cancerous human solid tissues. RNA. 2008 May; 14(5):844-52.Epub 2008 Mar. 28; each of which reference is herein incorporated byreference in its entirety.

Peptide nucleic acids (PNAs) which are a new class of synthetic nucleicacid analogs in which the phosphate-sugar polynucleotide backbone isreplaced by a flexible pseudo-peptide polymer may be used in analysis ofa biosignature. PNAs are capable of hybridizing with high affinity andspecificity to complementary RNA and DNA sequences and are highlyresistant to degradation by nucleases and proteinases. Peptide nucleicacids (PNAs) are an attractive new class of probes with applications incytogenetics for the rapid in situ identification of human chromosomesand the detection of copy number variation (CNV). Multicolor peptidenucleic acid-fluorescence in situ hybridization (PNA-FISH) protocolshave been described for the identification of several human CNV-relateddisorders and infectious diseases. PNAs can also be used as moleculardiagnostic tools to non-invasively measure oncogene mRNAs with tumortargeted radionuclide-PNA-peptide chimeras. Methods of using PNAs aredescribed further in Pellestor F et al, Curr Pharm Des. 2008;14(24):2439-44, Tian X et al, Ann N Y Acad Sci. 2005 November;1059:106-44, Paulasova P and Pellestor F, Annales de Génétique, 47(2004) 349-358, Stender H. Expert Rev Mol Diagn. 2003 September;3(5):649-55. Review, Vigneault et al., Nature Methods, 5(9), 777-779(2008), each reference is herein incorporated by reference in itsentirety. These methods can be used to screen the genetic materialsisolated from a vesicle. When applying these techniques to acell-of-origin specific vesicle, they can be used to identify a givenmolecular signal that directly pertains to the cell of origin.

Mutational analysis may be carried out for mRNAs and DNA, includingthose that are identified from a vesicle. For mutational analysis of atarget or biomarker that is of RNA origin, the RNA (mRNA, miRNA orother) can be reverse transcribed into cDNA and subsequently sequencedor assayed, such as for known SNPs (by Taqman SNP assays, for example)or single nucleotide mutations, as well as using sequencing to look forinsertions or deletions to determine mutations present in thecell-of-origin. Multiplexed ligation dependent probe amplification(MLPA) could alternatively be used for the purpose of identifying CNV insmall and specific areas of interest. For example, once the total RNAhas been obtained from isolated colon cancer-specific vesicles, cDNA canbe synthesized and primers specific for exons 2 and 3 of the KRAS genecan be used to amplify these two exons containing codons 12, 13 and 61of the KRAS gene. The same primers used for PCR amplification can beused for Big Dye Terminator sequence analysis on the ABI 3730 toidentify mutations in exons 2 and 3 of KRAS. Mutations in these codonsare known to confer resistance to drugs such as Cetuximab andPanitumimab. Methods of conducting mutational analysis are described inMaheswaran S et al, Jul. 2, 2008 (10.1056/NEJMoa0800668) and Orita, M etal, PNAS 1989, (86): 2766-70, each of which is herein incorporated byreference in its entirety.

Other methods of conducting mutational analysis include miRNAsequencing. Applications for identifying and profiling miRNAs can bedone by cloning techniques and the use of capillary DNA sequencing or“next-generation” sequencing technologies. The new sequencingtechnologies currently available allow the identification oflow-abundance miRNAs or those exhibiting modest expression differencesbetween samples, which may not be detected by hybridization-basedmethods. Such new sequencing technologies include the massively parallelsignature sequencing (MPSS) methodology described in Nakano et al. 2006,Nucleic Acids Res. 2006; 34:D731-D735. doi: 10.1093/nar/gkj077, theRoche/454 platform described in Margulies et al. 2005, Nature. 2005;437:376-380 or the Illumina sequencing platform described in Berezikovet al. Nat. Genet. 2006b; 38:1375-1377, each of which is incorporated byreference in its entirety.

Additional methods to determine a biosignature includes assaying abiomarker by allele-specific PCR, which includes specific primers toamplify and discriminate between two alleles of a gene simultaneously,single-strand conformation polymorphism (SSCP), which involves theelectrophoretic separation of single-stranded nucleic acids based onsubtle differences in sequence, and DNA and RNA aptamers. DNA and RNAaptamers are short oligonucleotide sequences that can be selected fromrandom pools based on their ability to bind a particular molecule withhigh affinity. Methods of using aptamers are described in Ulrich H etal, Comb Chem High Throughput Screen. 2006 September; 9(8):619-32,Ferreira C S et al, Anal Bioanal Chem. 2008 February; 390(4):1039-50,Ferreira C S et al, Tumour Biol. 2006; 27(6):289-301, each of which isherein incorporated by reference in its entirety.

Biomarkers can also be detected using fluorescence in situ hybridization(FISH). Methods of using FISH to detect and localize specific DNAsequences, localize specific mRNAs within tissue samples or identifychromosomal abnormalities are described in Shaffer D R et al, ClinCancer Res. 2007 Apr. 1; 13(7):2023-9, Cappuzo F et al, Journal ofThoracic Oncology, Volume 2, Number 5, May 2007, Moroni M et al, LancetOncol. 2005 May; 6(5):279-86, each of which is herein incorporated byreference in its entirety.

An illustrative schematic for analyzing a population of vesicles fortheir payload is presented in FIG. 2E. In an embodiment, the methods ofthe invention include characterizing a phenotype by capturing vesicles(6330) and determining a level of microRNA species contained therein(6331), thereby characterizing the phenotype (6332).

A biosignature comprising a circulating biomarker or vesicle cancomprise a binding agent thereto. The binding agent can be a DNA, RNA,aptamer, monoclonal antibody, polyclonal antibody, Fabs, Fab′, singlechain antibody, synthetic antibody, aptamer (DNA/RNA), peptoid, zDNA,peptide nucleic acid (PNA), locked nucleic acid (LNA), lectin, syntheticor naturally occurring chemical compounds (including but not limited todrugs and labeling reagents).

A binding agent can used to isolate or detect a vesicle by binding to acomponent of the vesicle, as described above. The binding agent can beused to detect a vesicle, such as for detecting a cell-of-originspecific vesicle. A binding agent or multiple binding agents canthemselves form a binding agent profile that provides a biosignature fora vesicle. For example, if a vesicle population is detected or isolatedusing two, three, four or more binding agents in a differentialdetection or isolation of a vesicle from a heterogeneous population ofvesicles, the particular binding agent profile for the vesiclepopulation provides a biosignature for the particular vesiclepopulation.

As an illustrative example, a vesicle for characterizing a cancer can bedetected with one or more binding agents including, but not limited to,PSA, PSMA, PCSA, PSCA, B7H3, EpCam, TMPRSS2, mAB 5D4, XPSM-A9, XPSM-A10,Galectin-3, E-selectin, Galectin-1, or E4 (IgG2a kappa), or anycombination thereof.

The binding agent can also be for a general vesicle biomarker, such as a“housekeeping protein” or antigen. The biomarker can be CD9, CD63, orCD81. For example, the binding agent can be an antibody for CD9, CD63,or CD81. The binding agent can also be for other proteins, such as fortissue specific or cancer specific vesicles. The binding agent can befor PCSA, PSMA, EpCam, B7H3, or STEAP. The binding agent can be for DR3,STEAP, epha2, TMEM211, MFG-E8, Annexin V, TF, unc93A, A33, CD24, NGAL,EpCam, MUC17, TROP2, or TETS. For example, the binding agent can be anantibody or aptamer for PCSA, PSMA, EpCam, B7H3, DR3, STEAP, epha2,TMEM211, MFG-E8, Annexin V, TF, unc93A, A33, CD24, NGAL, EpCam, MUC17,TROP2, or TETS.

Various proteins are not typically distributed evenly or uniformly on avesicle shell. Vesicle-specific proteins are typically more common,while cancer-specific proteins are less common. In some embodiments,capture of a vesicle is accomplished using a more common, lesscancer-specific protein, such as one or more housekeeping proteins orantigen or general vesicle antigen (e.g., a tetraspanin), and one ormore cancer-specific biomarkers and/or one or more cell-of-originspecific biomarkers is used in the detection phase. In anotherembodiment, one or more cancer-specific biomarkers and/or one or morecell-of-origin specific biomarkers are used for capture, and one or morehousekeeping proteins or antigen or general vesicle antigen (e.g., atetraspanin) is used for detection. In embodiments, the same biomarkeris used for both capture and detection. Different binding agents for thesame biomarker can be used, such as antibodies or aptamers that binddifferent epitopes of an antigen.

Additional cellular binding partners or binding agents may be identifiedby any conventional methods known in the art, or as described herein,and may additionally be used as a diagnostic, prognostic ortherapy-related marker. For example, vesicles can be detected using oneor more binding agent listed in Tables 3, 4 or 5 herein. For example,the binding agent can also be for a general vesicle biomarker, such as a“housekeeping protein” or antigen. The general vesicle biomarker can beCD9, CD63, or CD81, or other biomarker in Table 3. The binding agent canalso be for other proteins, such as for cell of origin specific orcancer specific vesicles. As a non-limiting example, in the case ofprostate cancer, the binding agent can be for PCSA, PSMA, EpCam, B7H3,RAGE or STEAP. The binding agent can be for a biomarker in Tabled 4-5.For example, the binding agent can be an antibody or aptamer for PCSA,PSMA, EpCam, B7H3, RAGE, STEAP or other biomarker in Tabled 4-5.

Various proteins may not be distributed evenly or uniformly on a vesiclesurface. For example, vesicle-specific proteins are typically morecommon, while cancer-specific proteins are less common. In someembodiments, capture of a vesicle is accomplished using a more common,less cancer-specific protein, such as a housekeeping protein or antigen,and cancer-specific proteins is used in the detection phase. Dependingon the sensitivity of the detection system, the opposite method can alsobe used wherein a large vesicle population is captured using a bindingagent to a general vesicle marker and then cell-specific vesicles aredetected with detection agents specific to a sub-population of interest.

Furthermore, additional cellular binding partners or binding agents maybe identified by any conventional methods known in the art, or asdescribed herein, and may additionally be used as a diagnostic,prognostic or therapy-related marker.

microRNA Functional Assay

As described above, microRNAs can be found circulating in bodily fluidssuch as blood encapsulated in microvesicles, HDL and LDL particles aswell as components of ribonucleoprotein complexes (RNPs). microRNA canbe detected using available technologies such as described herein orknown in the art, including without limitation RT-qPCR or nextgeneration sequencing. However, microRNA in a biologically active stateis bound and activated by one or more of the Argonaute (“Ago”) proteins(e.g., Ago1, Ago2, Ago3, or Ago4). One aspect of the invention isdirected to compositions and methods that enable detection of afunctional activity of a target microRNA within a biological sample in asingle reaction. For a review of the Ago family of proteins, see, Hockand Meister, Genome Biology, 2008, 9:210.

More particularly, a substrate, a synthetic RNA molecule, a label andRISC(RNA-Induced Silencing Complex) reaction buffer components, andoptionally one or more isolated Ago protein, are used to assess one ormore nucleic acid biomarkers (e.g., microRNAs). Examples of a substratethat can be used in the invention include but are not limited to aplanar substrate, microbead, column or the like to which a first sectionof a synthetic RNA molecule, e.g., the 3′ or 5′ end, is tethered viadirect or indirect linkage. Such substrates are disclosed herein orknown in the art. The linkage is performed using methods known in theart, e.g., amino-carboxy coupling such as described in Wittebolle etal., Optimisation of the amino-carboxy coupling of oligonucleotides tobeads used in liquid arrays, J Chem Tech Biotech 81:476-480 (2006); suchtechniques are readily known to a person having ordinary skill in theart.

Another portion of other the synthetic RNA molecule, e.g., the opposing3′ or 5′ end, is attached directly or indirectly to a label ordetectable molecule. The label is any molecule that is capable of beingdetected, and such labels or detectable molecules are known in the artand include without limitation: a fluorescent label, radiolabel orenzymatic label. Additional examples of such labels are disclosed hereinabove. In between the substrate-tethered portion and the labeledportion, the synthetic RNA molecule comprises a section or portion thatis complementary to a target microRNA of interest. As desired, thecomplementary section can be perfectly complementary to the targetmicroRNA, i.e., 100% complementary. The degree of association betweenthe complementary section and the target microRNA can be manipulated,e.g., to allow the recognition of one specific target microRNA or toallow promiscuous recognition, e.g., of a family of target microRNAs.Means for such manipulation are disclosed herein or are known in theart, e.g., base pair mismatches, or assay conditions such as temperatureor salt concentration. For example, the complementary section may carrymismatches with the target microRNA, e.g., such that the complementarysection is at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98% or at least 99% complementary to the targetmicroRNA. The method comprises contacting the labeled and tetheredsynthetic RNA molecule with a sample comprising or suspected to comprisethe target microRNA of interest. If the target microRNA is present inthe sample and is also bound to an Ago protein, the Ago-microRNA canassociate with the synthetic RNA molecule via base pairing between thetarget microRNA and the complementary region. Such associationfacilitates the cleavage of the synthetic RNA molecule via theendonucleolytic cleavage activity of the Ago protein. This cleavageliberates the label of the synthetic RNA molecule from the substrate.The amount of label associated with the substrate can be detected beforeand after contact with the sample comprising the target microRNA. Anysuch differences in the amount of label are indicative of the amount ofAgo-bound target microRNA in the input sample.

Useful reaction conditions and buffers for the assay are known in theart. The reaction be performed at room temperature, 25° C., 30° C., 37°C. or up to 42° C.-45° C. for anywhere from 5 min to overnight dependingon assay sensitivity and target abundance. For example, the reaction canbe performed for 1-2 h at 37° C. See, e.g., Brown et al., Targetaccessibility dictates the potency of human RISC. Nature Structural &Molecular Biology 12, 469-470 (2005); Robb et al., Specific and potentRNAi in the nucleus of human cells. Nature Structural & MolecularBiology 12, 133-137 (2005); Lima et al., Binding and CleavageSpecificities of Human Argonaute2. J. Biol. Chem. 2009 284: 26017-26028.

An exemplary embodiment of the assay is shown in FIG. 26. As shown inFIG. 26A, a synthetic RNA molecule contains a 3′ linker/extender region262, a central miRNA targeting region 263 and a second 5′linker/extension region 264. The RNA is attached to a substrate, heremicrobead 261, on the 3′ end 262 and the 5′ end 264 is conjugated withbiotin 266. The central miRNA targeting region 263 is designed tocomplement a miRNA sequence of interest. Region 263 can be complementaryto any microRNA of interest. In the example shown in FIG. 26,streptavidin-PE (Phycoerythrin) 265 is used to label the biotin end ofthe synthetic RNA. As described, other labeling schemes can be employed.For example, the 5′ end 264 can be directly labeled with Cy3, Cy5 orother detectable moiety disclosed herein or known in the art. As anotherexample, the 5′ end 264 can be indirectly labeled via base pairing withanother complementary oligonucleotide that is labeled. If the targetmicroRNA is present in the sample and is bound/associated with an Agoprotein 267, e.g., any of Ago1-4 in the sample or added thereto, such asrecombinant Agog (rAgo2), the target microRNA will bind thecomplementary microRNA targeting region 263 and subsequently cleave thesynthetic RNA at region 263 through the endonucleolytic cleavageactivity of Argonaute. See step 268 in FIG. 26. Once cleaved, thelabeled end (here 5′) of the synthetic RNA molecule is released, therebyseparating the biotin/Streptavidin-PE complex 265-266 from the microbead261. See FIG. 26B. Next, the substrate microbeads can be isolated andwashed to remove the cleaved and untethered end of the RNA, therebyleaving only the remaining uncleaved and still labeled material as wellas any cleaved but now unlabeled RNA. After this wash step, thedifference in PE signal correlates with the concentration and activityof the Ago-bound target microRNA 267 present in the original assay. Thequantity of Ago-bound target microRNA in the input sample determines thelevel of RNA cleaved. For example, if the target microRNA is notpresent, or it is present but not bound in a functional form with Ago,the synthetic RNA target region 263 will remain uncleaved and the signalstrength will be unchanged.

Any appropriate source of RNA and/or RNA pre-loaded into Argonaute canbe tested using the assay. For example, the input sample may be celllysate, bodily fluids, blood fractions (which may contain circulatingArgonaute such as Ago 2 bound to miRNAs), plasma, serum, or isolatedmicrovesicles. In some embodiments, Argonaute immunoprecipitated from asample is used as an input source of RNP complexes for the assay. If thetarget microRNA is present and loaded into Argonaute in any of theaforementioned sources, the synthetic target 263 is cleaved and thelabel (e.g., biotin-strepavidin-PE 265-266 in the example of FIG. 26) isreleased.

FIGS. 26C-E illustrate schematically various sources of RNA that can beused as input for the assay. FIG. 26C illustrates microRNA 268 bound toan Ago protein 269 to form a ribonucleic acid complex 267. The Agoprotein can be Ago1, Ago 2, Ago3 or Ago 4. FIG. 26D illustratesimmunoprecipitation of an Argonaute-microRNA complex 267 using a bindingagent to Ago 2610. The binding agent can be specific to a certainArgonaute, e.g., an antibody or aptamer to Agog. In other embodiments,the binding agent recognizes more than one Ago family member, e.g.,Ago1-4. In still other embodiments, the binding agent can bindindirectly to the one or more Ago protein. For example, the bindingagent for the immunoprecipitation can be an antibody or aptamer to GW182protein which forms a complex with Ago proteins. FIG. 26E illustratesdirect analysis of Argonaute-microRNA complex 267, e.g., from a celllysate, bodily fluid, or lysed microvesicle.

Alternately, the assay input can comprise RNA from a sample source boundthat is then contacted with an Ago protein, such as purified Agoincluding recombinant Ago (rAgo). In this manner, RNA can be isolatedfrom any appropriate source including without limitation cell lysate,bodily fluids, plasma, concentrated plasma, microvesicles, or HDL andLDL particles. Once isolated, the Ago protein, e.g., recombinantArgonaute 2, can be used to bind small RNA present in the sample. TheAgo bound RNA can be used as input into the assay.

As described above, the third portion of the synthetic RNA molecule islabeled and thus cleavage of the complementary section allows removal ofthe label from the substrate. Thus, the amount of label removed from thesubstrate corresponds to the number of cleavage events. It will beappreciated that alternate methods of detecting the cleavage events arewithin the scope of the invention. In one embodiment, the label is addedto the reaction mixture after the cleavage reaction has been allowed tooccur. Following the example above, the streptavidin-PE 265 is addedafter the cleavage reaction has taken place. In another example, thethird portion of the synthetic RNA molecule is not labeled. Rather, thecleavage events are observed by detecting the amount of cleavedsynthetic RNA molecule remaining on the column after the cleavagereaction has occurred.

The degree of label liberated from the substrate can be detected andcompared before and after the cleavage reaction has taken place.Alternately, the kinetics of the cleavage reaction can be observed usingthe subject methods. In an embodiment, the degree of label liberatedfrom the substrate is detected in real time, thereby revealing thekinetics of the cleavage reaction.

Using the microRNA functional assay, virtually any microRNA can bescreened with synthetic RNAs containing matched miRNA targeting regions.The assay can be performed in uniplex or multiplex fashion with multiplesynthetic targets attached to distinguishable microbeads.

In an embodiment, the miR assay system is used for therapeutic RNAimolecule delivery and mode of action confirmation. Here, RNAi moleculesare delivered systemically or in a targeted fashion to an appropriatecell type, tissue or other anatomical region. Target tissues can beanalyzed for confirmation of delivery and confirmation of the RNAitherapeutic mode of action. For example, the presence of a therapeuticRNAi molecule at the tissue of interest can be detected by a phenotypicresult directly driven by mRNA knockdown due to the activation of theRNAi therapeutic or alternatively through an unrelated apoptotic orinflammatory response of the cell. Lastly, IC50 of the activatedtherapeutic RNAi agent at the target tissue can be established usingthis methodology.

Biosignatures for Cancer

As described herein, biosignatures comprising circulating biomarkers canbe used to characterize a cancer. This Section presents a non-exclusivelist of biomarkers that can be used as part of a biosignature, e.g., forprostate, GI, or ovarian cancer. In some embodiments, the circulatingbiomarkers are associated with a vesicle or with a population ofvesicles. For example, circulating biomarkers associated with vesiclescan be used to capture and/or to detect a vesicle or a vesiclepopulation.

It will be appreciated that the biomarkers presented herein may beuseful in biosignatures for other diseases, e.g., other proliferativedisorders and cancers of other cellular or tissue origins. For example,transformation in various cell types can be due to common events, e.g.,mutation in p53 or other tumor suppressor. A biosignature comprisingcell-of-origin biomarkers and cancer biomarkers can be used to furtherassess the nature of the cancer. Biomarkers for metastatic cancer may beused with cell-of-origin biomarkers to assess a metastatic cancer. Suchbiomarkers for use with the invention include those in Dawood, Novelbiomarkers of metastatic cancer, Exp Rev Mol Diag July 2010, Vol. 10,No. 5, Pages 581-590, which publication is incorporated herein byreference in its entirety.

The biosignatures of the invention may comprise markers that areupregulated, downregulated, or have no change, depending on thereference. Solely for illustration, if the reference is a normal sample,the biosignature may indicate that the subject is normal if thesubject's biosignature is not changed compared to the reference.Alternately, the biosignature may comprise a mutated nucleic acid oramino acid sequence so that the levels of the components in thebiosignature are the same between a normal reference and a diseasedsample. In another case, the reference can be a cancer sample, such thatthe subject's biosignature indicates cancer if the subject'sbiosignature is substantially similar to the reference. The biosignatureof the subject can comprise components that are both upregulated anddownregulated compared to the reference. Solely for illustration, if thereference is a normal sample, a cancer biosignature can comprise bothupregulated oncogenes and downregulated tumor suppressors. Vesiclemarkers can also be differentially expressed in various settings. Forexample, tetraspanins may be overexpressed in cancer vesicles comparedto non-cancer vesicles, whereas MFG-E8 can be overexpressed innon-cancer vesicles as compared to cancer vesicles.

Theranosis

As disclosed herein, methods are disclosed for characterizing aphenotype for a subject by assessing one or more biomarkers, includingvesicle biomarkers and/or circulating biomarkers. The biomarkers can beassessed using methods for multiplexed analysis of vesicle biomarkersdisclosed herein. Characterizing a phenotype can include providing atheranosis for a subject, such as determining if a subject is predictedto respond to a treatment or is predicted to be non-responsive to atreatment. A subject that responds to a treatment can be termed aresponder whereas a subject that does not respond can be termed anon-responder. A subject suffering from a condition can be considered tobe a responder for a treatment based on, but not limited to, animprovement of one or more symptoms of the condition; a decrease in oneor more side effects of an existing treatment; an increased improvement,or rate of improvement, in one or more symptoms as compared to aprevious or other treatment; or prolonged survival as compared towithout treatment or a previous or other treatment. For example, asubject suffering from a condition can be considered to be a responderto a treatment based on the beneficial or desired clinical resultsincluding, but are not limited to, alleviation or amelioration of one ormore symptoms, diminishment of extent of disease, stabilized (i.e., notworsening) state of disease, preventing spread of disease, delay orslowing of disease progression, amelioration or palliation of thedisease state, and remission (whether partial or total), whetherdetectable or undetectable. Treatment also includes prolonging survivalas compared to expected survival if not receiving treatment or ifreceiving a different treatment.

The systems and methods disclosed herein can be used to select acandidate treatment for a subject in need thereof. Selection of atherapy can be based on one or more characteristics of a vesicle, suchas the biosignature of a vesicle, the amount of vesicles, or both.Vesicle typing or profiling, such as the identification of thebiosignature of a vesicle, the amount of vesicles, or both, can be usedto identify one or more candidate therapeutic agents for an individualsuffering from a condition. For example, vesicle profiling can be usedto determine if a subject is a non-responder or responder to aparticular therapeutic, such as a cancer therapeutic if the subject issuffering from a cancer.

Vesicle profiling can be used to provide a diagnosis or prognosis for asubject, and a therapy can be selected based on the diagnosis orprognosis. Alternatively, therapy selection can be directly based on asubject's vesicle profile. Furthermore, a subject's vesicle profile canbe used to follow the evolution of a disease, to evaluate the efficacyof a medication, adapt an existing treatment for a subject sufferingfrom a disease or condition, or select a new treatment for a subjectsuffering from a disease or condition.

A subject's response to a treatment can be assessed using biomarkers,including vesicles, microRNA, and other circulating biomarkers. In oneembodiment, a subject is determined, classified, or identified as anon-responder or responder based on the subject's vesicle profileassessed prior to any treatment. During pretreatment, a subject can beclassified as a non-responder or responder, thereby reducing unnecessarytreatment options, and avoidance of possible side effects fromineffective therapeutics. Furthermore, the subject can be identified asa responder to a particular treatment, and thus vesicle profiling can beused to prolong survival of a subject, improve the subject's symptoms orcondition, or both, by providing personalized treatment options. Thus, asubject suffering from a condition can have a biosignature generatedfrom vesicles and other circulating biomarkers using one or more systemsand methods disclosed herein, and the profile can then be used todetermine whether a subject is a likely non-responder or responder to aparticular treatment for the condition. Based on use of the biosignatureto predict whether the subject is a non-responder or responder to theinitially contemplated treatment, a particular treatment contemplatedfor treating the subject's condition can be selected for the subject, oranother potentially more optimal treatment can be selected.

In one embodiment, a subject suffering from a condition is currentlybeing treated with a therapeutic. A sample can be obtained from thesubject before treatment and at one or more timepoints during treatment.A biosignature including vesicles or other biomarkers from the samplescan be assessed and used to determine the subject's response to thedrug, such as based on a change in the biosignature over time. If thesubject is not responding to the treatment, e.g., the biosignature doesnot indicate that the patient is responding, the subject can beclassified as being non-responsive to the treatment, or a non-responder.Similarly, one or more biomarkers associated with a worsening conditionmay be detected such that the biosignature is indicative of patient'sfailure to respond favorably to the treatment. In another example, oneor more biomarkers associated with the condition remain the same despitetreatment, indicating that the condition is not improving. Thus, basedon the biosignature, a treatment regimen for the subject can be changedor adapted, including selection of a different therapeutic.

Alternatively, the subject can be determined to be responding to thetreatment, and the subject can be classified as being responsive to thetreatment, or a responder. For example, one or more biomarkersassociated with an improvement in the condition or disorder may bedetected. In another example, one or more biomarkers associated with thecondition changes, thus indicating an improvement. Thus, the existingtreatment can be continued. In another embodiment, even when there is anindication of improvement, the existing treatment may be adapted orchanged if the biosignature indicates that another line of treatment maybe more effective. The existing treatment may be combined with anothertherapeutic, the dosage of the current therapeutic may be increased, ora different candidate treatment or therapeutic may be selected. Criteriafor selecting the different candidate treatment can depend on thesetting. In one embodiment, the candidate treatment may have been knownto be effective for subjects with success on the existing treatment. Inanother embodiment, the candidate treatment may have been known to beeffective for other subjects with a similar biosignature.

In some embodiments, the subject is undergoing a second, third or moreline of treatment, such as cancer treatment. A biosignature according tothe invention can be determined for the subject prior to a second, thirdor more line of treatment, to determine whether a subject would be aresponder or non-responder to the second, third or more line oftreatment. In another embodiment, a biosignature is determined for thesubject during the second, third or more line of treatment, to determineif the subject is responding to the second, third or more line oftreatment.

The methods and systems described herein for assessing one or morevesicles can be used to determine if a subject suffering from acondition is responsive to a treatment, and thus can be used to select atreatment that improves one or more symptoms of the condition; decreasesone or more side effects of an existing treatment; increases theimprovement, or rate of improvement, in one or more symptoms as comparedto a previous or other treatment; or prolongs survival as compared towithout treatment or a previous or other treatment. Thus, the methodsdescribed herein can be used to prolong survival of a subject byproviding personalized treatment options, and/or may reduce unnecessarytreatment options and unnecessary side effects for a subject.

The prolonged survival can be an increased progression-free survival(PFS), which denotes the chances of staying free of disease progressionfor an individual or a group of individuals suffering from a disease,e.g., a cancer, after initiating a course of treatment. It can refer tothe percentage of individuals in the group whose disease is likely toremain stable (e.g., not show signs of progression) after a specifiedduration of time. Progression-free survival rates are an indication ofthe effectiveness of a particular treatment. In other embodiments, theprolonged survival is disease-free survival (DFS), which denotes thechances of staying free of disease after initiating a particulartreatment for an individual or a group of individuals suffering from acancer. It can refer to the percentage of individuals in the group whoare likely to be free of disease after a specified duration of time.Disease-free survival rates are an indication of the effectiveness of aparticular treatment. Two treatment strategies can be compared on thebasis of the disease-free survival that is achieved in similar groups ofpatients. Disease-free survival is often used with the term overallsurvival when cancer survival is described.

The candidate treatment selected by vesicle profiling as describedherein can be compared to a non-vesicle profiling selected treatment bycomparing the progression free survival (PFS) using therapy selected byvesicle profiling (period B) with PFS for the most recent therapy onwhich the subject has just progressed (period A). In one setting, aPFSB/PFSA ratio≧1.3 is used to indicate that the vesicle profilingselected therapy provides benefit for subject (see for example, RobertTemple, Clinical measurement in drug evaluation. Edited by Wu Ninganoand G. T. Thicker John Wiley and Sons Ltd. 1995; Von Hoff D. D. Clin CanRes. 4: 1079, 1999: Dhani et al. Clin Cancer Res. 15: 118-123, 2009).

Other methods of comparing the treatment selected by vesicle profilingcan be compared to a non-vesicle profiling selected treatment bydetermine response rate (RECIST) and percent of subjects withoutprogression or death at 4 months. The term “about” as used in thecontext of a numerical value for PFS means a variation of +/−ten percent(10%) relative to the numerical value. The PFS from a treatment selectedby vesicle profiling can be extended by at least 10%, 15%, 20%, 30%,40%, 50%, 60%, 70%, 80%, or at least 90% as compared to a non-vesicleprofiling selected treatment. In some embodiments, the PFS from atreatment selected by vesicle profiling can be extended by at least100%, 150%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or at leastabout 1000% as compared to a non-vesicle profiling selected treatment.In yet other embodiments, the PFS ratio (PFS on vesicle profilingselected therapy or new treatment/PFS on prior therapy or treatment) isat least about 1.3. In yet other embodiments, the PFS ratio is at leastabout 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, or 2.0. In yet otherembodiments, the PFS ratio is at least about 3, 4, 5, 6, 7, 8, 9 or 10.

Similarly, the DFS can be compared in subjects whose treatment isselected with or without determining a biosignature according to theinvention. The DFS from a treatment selected by vesicle profiling can beextended by at least 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or atleast 90% as compared to a non-vesicle profiling selected treatment. Insome embodiments, the DFS from a treatment selected by vesicle profilingcan be extended by at least 100%, 150%, 200%, 300%, 400%, 500%, 600%,700%, 800%, 900%, or at least about 1000% as compared to a non-vesicleprofiling selected treatment. In yet other embodiments, the DFS ratio(DFS on vesicle profiling selected therapy or new treatment/DFS on priortherapy or treatment) is at least about 1.3. In yet other embodiments,the DFS ratio is at least about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8,1.9, or 2.0. In yet other embodiments, the DFS ratio is at least about3, 4, 5, 6, 7, 8, 9 or 10.

In some embodiments, the candidate treatment selected by microvescileprofiling does not increase the PFS ratio or the DFS ratio in thesubject; nevertheless vesicle profiling provides subject benefit. Forexample, in some embodiments no known treatment is available for thesubject. In such cases, vesicle profiling provides a method to identifya candidate treatment where none is currently identified. The vesicleprofiling may extend PFS, DFS or lifespan by at least 1 week, 2 weeks, 3weeks, 4 weeks, 1 month, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 2 months, 9weeks, 10 weeks, 11 weeks, 12 weeks, 3 months, 4 months, 5 months, 6months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months,13 months, 14 months, 15 months, 16 months, 17 months, 18 months, 19months, 20 months, 21 months, 22 months, 23 months, 24 months or 2years. The vesicle profiling may extend PFS, DFS or lifespan by at least2½ years, 3 years, 4 years, 5 years, or more. In some embodiments, themethods of the invention improve outcome so that subject is inremission.

The effectiveness of a treatment can be monitored by other measures. Acomplete response (CR) comprises a complete disappearance of thedisease: no disease is evident on examination, scans or other tests. Apartial response (PR) refers to some disease remaining in the body, butthere has been a decrease in size or number of the lesions by 30% ormore. Stable disease (SD) refers to a disease that has remainedrelatively unchanged in size and number of lesions. Generally, less thana 50% decrease or a slight increase in size would be described as stabledisease. Progressive disease (PD) means that the disease has increasedin size or number on treatment. In some embodiments, vesicle profilingaccording to the invention results in a complete response or partialresponse. In some embodiments, the methods of the invention result instable disease. In some embodiments, the invention is able to achievestable disease where non-vesicle profiling results in progressivedisease.

The theranosis based on a biosignature of the invention can be for aphenotype including without limitation those listed herein.Characterizing a phenotype includes determining a theranosis for asubject, such as predicting whether a subject is likely to respond to atreatment (“responder”) or be non-responsive to a treatment(“non-responder”). As used herein, identifying a subject as a“responder” to a treatment or as a “non-responder” to the treatmentcomprises identifying the subject as either likely to respond to thetreatment or likely to not respond to the treatment, respectively, anddoes not require determining a definitive prediction of the subject'sresponse. One or more vesicles, or populations of vesicles, obtainedfrom subject are used to determine if a subject is a non-responder orresponder to a particular therapeutic, by assessing biomarkers disclosedherein, e.g., those listed in Table 7. Detection of a high or lowexpression level of a biomarker, or a mutation of a biomarker, can beused to select a candidate treatment, such as a pharmaceuticalintervention, for a subject with a condition. Table 7 containsillustrative conditions and pharmaceutical interventions for thoseconditions. The table lists biomarkers that affect the efficacy of theintervention. The biomarkers can be assessed using the methods of theinvention, e.g., as circulating biomarkers or in association with avesicle.

TABLE 7 Examples of Biomarkers and Pharmaceutical Intervention for aCondition Condition Pharmaceutial intervention Biomarker PeripheralArterial Atorvastatin, Simvastatin, Rosuvastatin, C-reactiveprotein(CRP), serum Disease Pravastatin, Fluvastatin, LovastatinAmylyoid A (SAA), interleukin-6, intracellular adhesion molecule (ICAM),vascular adhesion molecule (VCAM), CD40L, fibrinogen, fibrin D-dimer,fibrinopeptide A, von Willibrand factor, tissue plasminogen activatorantigen (t-PA), factor VII, prothrombin fragment 1, oxidized low densitylipoprotein (oxLDL), lipoprotein A Non-Small Cell Erlotinib,Carboplatin, Paclitaxel, Gefitinib EGFR, excision repair cross- LungCancer complementation group 1 (ERCC1), p53, Ras, p27, class III betatubulin, breast cancer gene 1 (BRCA1), breast cancer gene 1 (BRCA2),ribonucleotide reductase messenger 1 (RRM1) Colorectal CancerPanitumumab, Cetuximab K-ras Breast Cancer Trastuzumab, Anthracyclines,Taxane, HER2, toposiomerase II alpha, Methotrexate, fluorouracilestrogen receptor, progesterone receptor Alzheimer's Disease Donepezil,Galantamine, Memantine, beta-amyloid protein, amyloid Rivastigmine,Tacrine precursor protein (APP), APP670/671, APP693, APP692, APP715,APP716, APP717, APP723, presenilin 1, presenilin 2, cerebrospinal fluidamyloid beta protein 42 (CSF-Abeta42), cerebrospinal fluid amyloid betaprotein 40 (CSF-Abeta40), F2 isoprostane, 4-hydroxynonenal, F4neuroprostane, acrolein Arrhythmia Disopyramide, Flecainide, Lidocaine,Mexiletine, SERCA, AAP, Connexin 40, Moricizine, Procainamide,Propafenone, Connexin 43, ATP-sensitive Quinidine, Tocainide,Acebutolol, Atenolol, potassium channel, Kv1.5 channel, Betaxolol,Bisoprolol, Carvedilol, Esmolol, acetylcholine-activated posassiumMetoprolol, Nadolol, Propranolol, Sotalol, channel Timolol, Amiodarone,Azimilide, Bepridil, Dofetilide, Ibutilide, Tedisamil, Diltiazem,Verapamil, Azimilide, Dronedarone, Amiodarone, PM101, ATI-2042,Tedisamil, Nifekalant, Ambasilide, Ersentilide, Trecetilide, Almokalant,D-sotalol, BRL-32872, HMR1556, L768673, Vernakalant, AZD70009, AVE0118,S9947, NIP-141/142, XEN-D0101/2, Ranolazine, Pilsicainide, JTV519,Rotigaptide, GAP-134 Rheumatoid arthritis Methotrexate, infliximab,adalimumab, 677CC/1298AA MTHFR, etanercept, sulfasalazine 677CT/1298ACMTHFR, 677CT MTHFR, G80AA RFC-1, 3435TT MDR1 (ABCB1), 3435TT ABCB1,AMPD1/ATIC/ITPA, IL1-RN3, HLA-DRB103, CRP, HLA-D4, HLA DRB-1,anti-citrulline epitope containing peptides, anti-A1/RA33, Erythrocytesedimentation rate (ESR), C-reactive protein (CRP), SAA (serumamyloid-associated protein), rheumatoid factor, IL-1, TNF, IL-6, IL-8,IL-1Ra, Hyaluronic acid, Aggrecan, Glc- Gal-PYD, osteoprotegerin, RNAKL,carilage oligomeric matrix protein (COMP), calprotectin ArterialFibrillation warfarin, aspirin, anticoagulants, heparin, F1.2, TAT, FPA,beta- ximelagatran throboglobulin, platelet factor 4, solubleP-selectin, IL-6, CRP HIV Infection Zidovudine, Didanosine, Zalcitabine,Stavudine, HIV p24 antigen, TNF-alpha, Lamivudine, Saquinavir,Ritonavir, Indinavir, TNFR-II, CD3, CD14, CD25, Nevirane, Nelfinavir,Delavirdine, Stavudine, CD27, Fas, FasL, beta2 Efavirenz, Etravirine,Enfuvirtide, Darunavir, microglobulin, neopterin, HIV Abacavir,Amprenavir, Lonavir/Ritonavirc, RNA, HLA-B *5701 Tenofovir, TipranavirCardiovascular lisinopril, candesartan, enalapril ACE inhibitor,angiotensin Disease

Cancer

Vesicle biosignatures can be used in the theranosis of a cancer, such asidentifying whether a subject suffering from cancer is a likelyresponder or non-responder to a particular cancer treatment. The subjectmethods can be used to theranose cancers including those listed herein,e.g., in the “Phenotype” section above. These include without limitationlung cancer, non-small cell lung cancer small cell lung cancer(including small cell carcinoma (oat cell cancer), mixed smallcell/large cell carcinoma, and combined small cell carcinoma), coloncancer, breast cancer, prostate cancer, liver cancer, pancreatic cancer,brain cancer, kidney cancer, ovarian cancer, stomach cancer, melanoma,bone cancer, gastric cancer, breast cancer, glioma, glioblastoma,hepatocellular carcinoma, papillary renal carcinoma, head and necksquamous cell carcinoma, leukemia, lymphoma, myeloma, or other solidtumors.

A biosignature of circulating biomarkers, including markers associatedwith vesicle, in a sample from a subject suffering from a cancer can beused select a candidate treatment for the subject. The biosignature canbe determined according to the methods of the invention presentedherein. In some embodiments, the candidate treatment comprises astandard of care for the cancer. The biosignature can be used todetermine if a subject is a non-responder or responder to a particulartreatment or standard of care. The treatment can be a cancer treatmentsuch as radiation, surgery, chemotherapy or a combination thereof. Thecancer treatment can be a therapeutic such as anti-cancer agents andchemotherapeutic regimens. Cancer treatments for use with the methods ofthe invention include without limitation those listed in Table 8:

TABLE 8 Cancer Treatments Treatment or Agent Cancer therapies Radiation,Surgery, Chemotherapy, Biologic therapy, Neo-adjuvant therapy, Adjuvanttherapy, Palliative therapy, Watchful waiting Anti-cancer agents13-cis-Retinoic Acid, 2-CdA, 2-Chlorodeoxyadenosine, 5-Azacitidine,5-Fluorouracil, (chemotherapies and 5-FU, 6-Mercaptopurine, 6-MP, 6-TG,6-Thioguanine, Abraxane, Accutane ®, biologics) Actinomycin-D,Adriamycin ®, Adrucil ®, Afinitor ®, Agrylin ®, Ala-Cort ®, Aldesleukin,Alemtuzumab, ALIMTA, Alitretinoin, Alkaban-AQ ®, Alkeran ®, All-transretinoic Acid, Alpha Interferon, Altretamine, Amethopterin,Amifostine, Aminoglutethimide, Anagrelide, Anandron ®, Anastrozole,Arabinosylcytosine, Ara-C, Aranesp ®, Aredia ®, Arimidex ®, Aromasin ®,Arranon ®, Arsenic Trioxide, Asparaginase, ATRA, Avastin ®, Azacitidine,BCG, BCNU, Bendamustine, Bevacizumab, Bexarotene, BEXXAR ®,Bicalutamide, BiCNU, Blenoxane ®, Bleomycin, Bortezomib, Busulfan,Busulfex ®, C225, Calcium Leucovorin, Campath ®, Camptosar ®,Camptothecin-11, Capecitabine, Carac ™, Carboplatin, Carmustine,Carmustine Wafer, Casodex ®, CC-5013, CCI-779, CCNU, CDDP, CeeNU,Cerubidine ®, Cetuximab, Chlorambucil, Cisplatin, Citrovorum Factor,Cladribine, Cortisone, Cosmegen ®, CPT-11, Cyclophosphamide, Cytadren ®,Cytarabine, Cytarabine Liposomal, Cytosar-U ®, Cytoxan ®, Dacarbazine,Dacogen, Dactinomycin, Darbepoetin Alfa, Dasatinib, DaunomycinDaunorubicin, Daunorubicin Hydrochloride, Daunorubicin Liposomal,DaunoXome ®, Decadron, Decitabine, Delta-Cortef ®, Deltasone ®,Denileukin, Diftitox, DepoCyt ™, Dexamethasone, Dexamethasone AcetateDexamethasone Sodium Phosphate, Dexasone, Dexrazoxane, DHAD, DIC, DiodexDocetaxel, Doxil ®, Doxorubicin, Doxorubicin Liposomal, Droxia ™, DTIC,DTIC- Dome ®, Duralone ®, Efudex ®, Eligard ™, Ellence ™, Eloxatin ™,Elspar ®, Emcyt ®, Epirubicin, Epoetin Alfa, Erbitux, Erlotinib, ErwiniaL-asparaginase, Estramustine, Ethyol Etopophos ®, Etoposide, EtoposidePhosphate, Eulexin ®, Everolimus, Evista ®, Exemestane, Fareston ®,Faslodex ®, Femara ®, Filgrastim, Floxuridine, Fludara ®, Fludarabine,Fluoroplex ®, Fluorouracil, Fluorouracil (cream), Fluoxymesterone,Flutamide, Folinic Acid, FUDR ®, Fulvestrant, G-CSF, Gefitinib,Gemcitabine, Gemtuzumab ozogamicin, Gemzar, Gleevec ™, Gliadel ® Wafer,GM-CSF, Goserelin, Granulocyte - Colony Stimulating Factor, GranulocyteMacrophage Colony Stimulating Factor, Halotestin ®, Herceptin ®,Hexadrol, Hexalen ®, Hexamethylmelamine, HMM, Hycamtin ®, Hydrea ®,Hydrocort Acetate ®, Hydrocortisone, Hydrocortisone Sodium Phosphate,Hydrocortisone Sodium Succinate, Hydrocortone Phosphate, Hydroxyurea,Ibritumomab, Ibritumomab, Tiuxetan, Idamycin ®, Idarubicin, Ifex ®,IFN-alpha, Ifosfamide, IL-11, IL-2, Imatinib mesylate, ImidazoleCarboxamide, Interferon alfa, Interferon Alfa-2b (PEG Conjugate),Interleukin-2, Interleukin-11, Intron A ® (interferon alfa-2b),Iressa ®, Irinotecan, Isotretinoin, Ixabepilone, Ixempra ™, Kidrolase(t), Lanacort ®, Lapatinib, L-asparaginase, LCR, Lenalidomide,Letrozole, Leucovorin, Leukeran, Leukine ™, Leuprolide, Leurocristine,Leustatin ™, Liposomal Ara-C Liquid Pred ®, Lomustine, L-PAM,L-Sarcolysin, Lupron ®, Lupron Depot ®, Matulane ®, Maxidex,Mechlorethamine, Mechlorethamine Hydrochloride, Medralone ®, Medrol ®,Megace ®, Megestrol, Megestrol Acetate, Melphalan, Mercaptopurine,Mesna, Mesnex ™, Methotrexate, Methotrexate Sodium, Methylprednisolone,Meticorten ®, Mitomycin, Mitomycin-C, Mitoxantrone, M-Prednisol ®, MTC,MTX, Mustargen ®, Mustine, Mutamycin ®, Myleran ®, Mylocel ™,Mylotarg ®, Navelbine ®, Nelarabine, Neosar ®, Neulasta ™, Neumega ®,Neupogen ®, Nexavar ®, Nilandron ®, Nilutamide, Nipent ®, NitrogenMustard, Novaldex ®, Novantrone ®, Octreotide, Octreotide acetate,Oncospar ®, Oncovin ®, Ontak ®, Onxal ™, Oprevelkin, Orapred ®,Orasone ®, Oxaliplatin, Paclitaxel, Paclitaxel Protein-bound,Pamidronate, Panitumumab, Panretin ®, Paraplatin ®, Pediapred ®, PEGInterferon, Pegaspargase, Pegfilgrastim, PEG-INTRON ™,PEG-L-asparaginase, PEMETREXED, Pentostatin, Phenylalanine Mustard,Platinol ®, Platinol-AQ ®, Prednisolone, Prednisone, Prelone ®,Procarbazine, PROCRIT ®, Proleukin ®, Prolifeprospan 20 with CarmustineImplant, Purinethol ®, Raloxifene, Revlimid ®, Rheumatrex ®, Rituxan ®,Rituximab, Roferon-A ® (Interferon Alfa-2a), Rubex ®, Rubidomycinhydrochloride, Sandostatin ®, Sandostatin LAR ®, Sargramostim,Solu-Cortef ®, Solu-Medrol ®, Sorafenib, SPRYCEL ™, STI-571,Streptozocin, SU11248, Sunitinib, Sutent ®, Tamoxifen, Tarceva ®,Targretin ®, Taxol ®, Taxotere ®, Temodar ®, Temozolomide, Temsirolimus,Teniposide, TESPA, Thalidomide, Thalomid ®, TheraCys ®, Thioguanine,Thioguanine Tabloid ®, Thiophosphoamide, Thioplex ®, Thiotepa, TICE ®,Toposar ®, Topotecan, Toremifene, Torisel ®, Tositumomab, Trastuzumab,Treanda ®, Tretinoin, Trexall ™, Trisenox ®, TSPA, TYKERB ®, VCR,Vectibix ™, Velban ®, Velcade ®, VePesid ®, Vesanoid ®, Viadur ™,Vidaza ®, Vinblastine, Vinblastine Sulfate, Vincasar Pfs ®, Vincristine,Vinorelbine, Vinorelbine tartrate, VLB, VM-26, Vorinostat, VP-16,Vumon ®, Xeloda ®, Zanosar ®, Zevalin ™, Zinecard ®, Zoladex ®,Zoledronic acid, Zolinza, Zometa ® Combination CHOP (cyclophosphamide,doxorubicin, vincristine, and prednisone); CVP Therapies(cyclophosphamide, vincristine, and prednisone); RCVP (Rituximab + CVP);RCHOP (Rituximab + CHOP); RICE (Rituximab + ifosamide, carboplatin,etoposide); RDHAP, (Rituximab + dexamethasone, cytarabine, cisplatin);RESHAP (Rituximab + etoposide, methylprednisolone, cytarabine,cisplatin); combination treatment with vincristine, prednisone, andanthracycline, with or without asparaginase; combination treatment withdaunorubicin, vincristine, prednisone, and asparaginase; combinationtreatment with teniposide and Ara-C (cytarabine); combination treatmentwith methotrexate and leucovorin; combination treatment with bleomycin,doxorubicin, etoposide, mechlorethamine, prednisone, vinblastine, andvincristine; FOLFOX4 regimen (oxaliplatin, leucovorin, and fluorouracil[5-FU]); FOLFIRI regimen (Irinotecan Hydrochloride, Fluorouracil, andLeucovorin Calcium); Levamisole regimen (5-FU and levamisole); NCCTGregimen (5-FU and low-dose leucovorin); NSABP regimen (5-FU andhigh-dose leucovorin); XAD (Xelox (Capecitabine + Oxaliplatin) +Bevacizumab + Dasatinib); FOLFOX/Bevacizumab/Hydroxychloroquine; GermanAIO regimen (folic acid, 5-FU, and irinotecan); Douillard regimen (folicacid, 5-FU, and irinotecan); CAPOX regimen (Capecitabine, oxaliplatin);FOLFOX6 regimen (oxaliplatin, leucovorin, and 5-FU); FOLFIRI regimen(folic acid, 5-FU, and irinotecan); FUFOX regimen (oxaliplatin,leucovorin, and 5-FU); FUOX regimen (oxaliplatin and 5-FU); IFL regimen(irinotecan, 5-FU, and leucovorin); XELOX regimen (capecitabineoxaliplatin); KHAD-L (ketoconazole, hydrocortisone, dutasteride andlapatinib); Biologics anti-CD52 antibodies (e.g., Alemtuzumab),anti-CD20 antibodies (e.g., Rituximab), anti-CD40 antibodies (e.g.,SGN40) Classes of Anthracyclines and related substances, Anti-androgens,Anti-estrogens, Antigrowth Treatments hormones (e.g., Somatostatinanalogs), Combination therapy (e.g., vincristine, bcnu, melphalan,cyclophosphamide, prednisone (VBMCP)), DNA methyltransferase inhibitors,Endocrine therapy - Enzyme inhibitor, Endocrine therapy - other hormoneantagonists and related agents, Folic acid analogs (e.g., methotrexate),Folic acid analogs (e.g., pemetrexed), Gonadotropin releasing hormoneanalogs, Gonadotropin- releasing hormones, Monoclonal antibodies(EGFR-Targeted - e.g., panitumumab, cetuximab), Monoclonal antibodies(Her2-Targeted - e.g., trastuzumab), Monoclonal antibodies(Multi-Targeted - e.g., alemtuzumab), Other alkylating agents,Antineoplastic agents (e.g., asparaginase, ATRA, bexarotene, celecoxib,gemcitabine, hydroxyurea, irinotecan, topotecan, pentostatin), Cytotoxicantibiotics, Platinum compounds, Podophyllotoxin derivatives (e.g.,etoposide), Progestogens, Protein kinase inhibitors (EGFR-Targeted),Protein kinase inhibitors (Her2 targeted therapy - e.g., lapatinib),Pyrimidine analogs (e.g., cytarabine), Pyrimidine analogs (e.g.,fluoropyrimidines), Salicylic acid and derivatives (e.g., aspirin),Src-family protein tyrosine kinase inhibitors (e.g., dasatinib), Taxanes(e.g., nab-paclitaxel), Vinca Alkaloids and analogs, Vitamin D andanalogs, Monoclonal antibodies (Multi-Targeted - e.g., bevacizumab),Protein kinase inhibitors (e.g., imatinib, sorafenib, sunitinib)Prostate Cancer Watchful waiting (i.e., monitor without treatment);Surgery (e.g., Pelvic Treatments lymphadenectomy, Radical prostatectomy,Transurethral resection of the prostate (TURP); Orchiectomy); Radiationtherapy (e.g., external-beam radiation therapy (EBRT), Proton beamradiation; implantation of radioisotopes (i.e., iodine I 125, palladium,and iridium)); Hormone therapy (e.g., Luteinizing hormone-releasinghormone agonists such as leuprolide, goserelin, buserelin or ozarelix;Antiandrogens such as flutamide, 2-hydroxyflutamide, bicalutamide,megestrol acetate, nilutamide, ketoconazole, aminoglutethimide;calcitriol, gonadotropin-releasing hormone (GnRH), estrogens (DES,chlorotrianisene, ethinyl estradiol, conjugated estrogens USP, and DES-diphosphate), triptorelin, finasteride, cyproterone acetate, ASP3550);Cryosurgery/cryotherapy; Chemotherapy and Biologic therapy (dutasteride,zoledronate, azacitidine, docetaxel, prednisolone, celecoxib,atorvastatin, AMT2003, soy protein, LHRH agonist, PD-103, pomegranateextract, soy extract, taxotere, I-125, zoledronic acid, dasatinib,vitamin C, vitamin D, vitamin D3, vitamin E, gemcitabine, cisplatin,lenalidomide, prednisone, degarelix, OGX-011, OGX-427, MDV3100,tasquinimod, cabazitaxel, TOOKAD ®, lanreotide, PROSTVAC, GM-CSF,lenalidomide, samarium Sm-153 lexidronam, N-Methyl-D-Aspartate(NMDA)-Receptor Antagonist, sorafenib, sorafenib tosylate, mitoxantrone,ABI-008, hydrocortisone, panobinostat, soy-tomato extract, KHAD-L,TOK-001, cixutumumab, temsirolimus, ixabepilone, TAK-700, TAK-448,TRC105, cyclophosphamide, lenalidomide, MLN8237, GDC-0449, Alpharadin ®,ARN-509, PX-866, ISIS EIF4E Rx, AEZS-108, 131I-F16SIP MonoclonalAntibody, anti-OX40 antibody, Muscadine Plus, ODM-201, BBI608, ZD4054,erlotinib, rIL-2, epirubicin, estramustine phosphate, HuJ591-GSmonoclonal (177Lu-J591), abraxane, IVIG, fermented wheat germ nutriment(FWGE), 153Sm-EDTMP, estramustine, mitoxantrone, vinblastine,carboplatin, paclitaxel, pazopanib, cytarabine, testosteronereplacement, Zoledronic Acid, Strontium Chloride Sr 89, paricalcitol,satraplatin, RAD001 (everolimus), valproic acid, tea extract, Hamsa-1,hydroxychloroquine, sipuleucel-T, selenomethionine, selenium, lycopene,sunitinib, vandetanib, IMC-A12 antibody, monoclonal antibody IMC-3G3,ixabepilone, diindolylmethane, metformin, efavirenz, dasatinib,nilutamide, abiraterone, cabozantinib (XL184), isoflavines, cinacalcethydrochloride, SB939, LY2523355, KX2-391, olaparib, genestein, digoxin,RO4929097, ipilimumab, bafetinib, cediranib maleate, MK2206, phenelzinesulfate, triptorelin pamoate, saracatinib, STA-9090, tesetaxel,pasireotide, afatinib, GTx 758, lonafarnib, satraplatin, radiolabeledantibody 7E11, FP253/fludarabine, Coxsackie A21 (CVA21) virus, ARRY-380,ARRY-382, anti- PSMA designer T cells, pemetrexed disodium, bortezomib,MDX-1106, white button mushroom extract, SU011248, MLN9708, BMTP-11,ABT-888, CX-4945, 4SC-205, temozolomide, MGAH22, vinorelbine ditartrate,Sodium Selenite, vorinostat, Ad- REIC/Dkk-3, ASG-5ME, IMF-001,PROHIBITIN-TP01, DSTP3086S, ridaforolimus, MK-2206, MK-0752,polyunsaturated fatty acids, I-125, statins, cholecalciferol, omega- 3fatty acids, raloxifene, etoposide, POMELLA ™ extract, Lucrin depot);Cancer vaccines (e.g., DNA vaccines, peptide vaccines, dendritic cellvaccines, PEP223, PSA/TRICOM, PROSTVAC-V/TRICOM, PROSTVAC-F/TRICOM, PSAvaccine, TroVax ®, GI-6207, PSMA and TARP Peptide Vaccine); Ultrasound;Proton beam radiation Colorectal Cancer Primary Surgical Therapy (e.g.,local excision; resection and anastomosis of primary Treatments lesionand removal of surrounding lymph nodes); Adjuvant Therapy (e.g.,fluorouracil (5-FU), capecitabine, leucovorin, oxaliplatin, erlotinib,irinotecan, aspirin, mitomycin C, suntinib, cetuximab, bevacizumab,pegfilgrastim, panitumumab, ramucirumab, curcumin, celecoxib, FOLFOX4regimen, FOLFOX6 regimen, FOLFIRI regimen, FUFOX regimen, FUOX regimen,IFL regimen, XELOX regimen, 5-FU and levamisole regimens, German AIOregimen, CAPOX regimen, Douillard regimen, XAD, RAD001 (everolimus), ARQ197, BMS-908662, JI-101, hydroxychloroquine (HCQ), Yttrium Microspheres,EZN-2208, CS-7017, IMC-1121B, IMC-18F1, docetaxel, lonafarnib,Maytansinoid DM4-Conjugated Humanized Monoclonal Antibody huC242,paclitaxel, ARRY-380, ARRY-382, IMO-2055, MDX1105-01, CX-4945,Pazopanib, Ixabepilone, OSI-906, NPC-1C Chimeric Monoclonal Antibody,brivanib, Poly-ADP Ribose (PARP) Inhibitor, RO4929097, Anti-cancervaccine, CEA vaccine, cyclophosphamide, yttrium Y 90 DOTA anti-CEAmonoclonal antibody M5A, MEHD7945A, ABT-806, ABT-888, MEDI-565,LY2801653, AZD6244, PRI-724, BKM120, tivozanib, floxuridine,dexamethosone, NKTR-102, perifosine, regorafenib, EP0906, Celebrex,PHY906, KRN330, imatinib mesylate, azacitidine, entinostat, PX-866,ABX-EGF, BAY 43-9006, ESO-1 Lymphocytes and Aldesleukin, LBH589,olaparib, fostamatinib, PD 0332991, STA-9090, cholecalciferol, GI-4000,IL-12, AMG 706, temsirolimus, dulanermin, bortezomib, ursodiol,ridaforolimus, veliparib, NK012, Dalotuzumab, MK-2206, MK- 0752,lenalidomide, REOLYSIN ®, AUY922, PRI-724, BKM120, avastin, dasatinib);Adjuvant Radiation Therapy (particularly for rectal cancer)

As shown in Table 8, cancer treatments include various surgical andtherapeutic treatments. Anti-cancer agents include drugs such as smallmolecules and biologicals. The methods of the invention can be used toidentify a biosignature comprising circulating biomarkers that can thenbe used for theranostic purposes such as monitoring a treatmentefficacy, classifying a subject as a responder or non-responder to atreatment, or selecting a candidate therapeutic agent. The invention canbe used to provide a theranosis for any cancer treatments, includingwithout limitation thernosis involving the cancer treatments in Tables8-10. Cancer therapies that can be identified as candidate treatments bythe methods of the invention include without limitation thechemotherapeutic agents listed in Tables 8-10 and any appropriatecombinations thereof. In one embodiment, the treatments are specific fora specific type of cancer, such as the treatments listed for prostatecancer, colorectal cancer, breast cancer and lung cancer in Table 8. Inother embodiments, the treatments are specific for a tumor regardless ofits origin but that displays a certain biosignature, such as abiosignature comprising a marker listed in Tables 9-10.

The invention provides methods of monitoring a cancer treatmentcomprising identifying a series of biosignatures in a subject over atime course, such as before and after a treatment, or over time afterthe treatment. The biosignatures are compared to a reference todetermine the efficacy of the treatment. In an embodiment, the treatmentis selected from Tables 8-10, such as radiation, surgery, chemotherapy,biologic therapy, neo-adjuvant therapy, adjuvant therapy, or watchfulwaiting. The reference can be from another individual or group ofindividuals or from the same subject. For example, a subject with abiosignature indicative of a cancer pre-treatment may have abiosignature indicative of a healthy state after a successful treatment.Conversely, the subject may have a biosignature indicative of cancerafter an unsuccessful treatment. The biosignatures can be compared overtime to determine whether the subject's biosignatures indicate animprovement, worsening of the condition, or no change. Additionaltreatments may be called for if the cancer is worsening or there is nochange over time. For example, hormone therapy may be used in additionto surgery or radiation therapy to treat more aggressive prostatecancers. One or more of the following miRs can be used in a biosignaturefor monitoring an efficacy of prostate cancer treatment: hsa-miR-1974,hsa-miR-27b, hsa-miR-103, hsa-miR-146a, hsa-miR-22, hsa-miR-382,hsa-miR-23a, hsa-miR-376c, hsa-miR-335, hsa-miR-142-5p, hsa-miR-221,hsa-miR-142-3p, hsa-miR-151-3p, hsa-miR-21, hsa-miR-16. One or more miRslisted in the following publication can be used in a biosignature formonitoring treatment of a cancer of the GI tract: Albulescu et al.,Tissular and soluble miRNAs for diagnostic and therapy improvement indigestive tract cancers, Exp Rev Mol Diag, 11:1, 101-120.

In some embodiments, the invention provides a method of identifying abiosignature in a sample from a subject in order to select a candidatetherapeutic. For example, the biosignature may indicate that adrug-associated target is mutated or differentially expressed, therebyindicating that the subject is likely to respond or not respond tocertain treatments. The candidate treatments can be chosen from theanti-cancer agents or classes of therapeutic agents identified in Tables8-10. In some embodiments, the candidate treatments identified accordingto the subject methods are chosen from at least the groups of treatmentsconsisting of 5-fluorouracil, abarelix, alemtuzumab, aminoglutethimide,anastrozole, asparaginase, aspirin, ATRA, azacitidine, bevacizumab,bexarotene, bicalutamide, calcitriol, capecitabine, carboplatin,celecoxib, cetuximab, chemotherapy, cholecalciferol, cisplatin,cytarabine, dasatinib, daunorubicin, decitabine, doxorubicin,epirubicin, erlotinib, etoposide, exemestane, flutamide, fulvestrant,gefitinib, gemcitabine, gonadorelin, goserelin, hydroxyurea, imatinib,irinotecan, lapatinib, letrozole, leuprolide, liposomal-doxorubicin,medroxyprogesterone, megestrol, megestrol acetate, methotrexate,mitomycin, nab-paclitaxel, octreotide, oxaliplatin, paclitaxel,panitumumab, pegaspargase, pemetrexed, pentostatin, sorafenib,sunitinib, tamoxifen, taxanes, temozolomide, toremifene, trastuzumab,VBMCP, and vincristine.

Similar to selecting a candidate treatment, the invention also providesa method of determining whether to treat a cancer at all. For example,prostate cancer can be a non-aggressive disease that is unlikely tosubstantially harm the subject. Radiation therapy with androgen ablation(hormone reduction) is the standard method of treating locally advancedprostate cancer. Morbidities of hormone therapy include impotence, hotflashes, and loss of libido. In addition, a treatment such asprostatectomy can have morbidities such as impotence or incontinence.Therefore, the invention provides biosignatures that indicateaggressiveness or a progression (e.g., stage or grade) of the cancer. Anon-aggressive cancer or localized cancer might not require immediatetreatment but rather be watched, e.g., “watchful waiting” of a prostatecancer. Whereas an aggressive or advanced stage lesion would require aconcomitantly more aggressive treatment regimen.

Examples of biomarkers that can be detected, and treatment agents thatcan be selected or possibly avoided are listed in Table 9. For example,a biosignature is identified for a subject with a prostate cancer,wherein the biosignature comprises levels of androgen receptor (AR).Overexpression or overproduction of AR, such as high levels of mRNAlevels or protein levels in a vesicle, provides an identification ofcandidate treatments for the subject. Such treatments include agents fortreating the subject such as Bicalutamide, Flutamide, Leuprolide, orGoserelin. The subject is accordingly identified as a responder toBicalutamide, Flutamide, Leuprolide, or Goserelin. In anotherillustrative example, BCRP mRNA, protein, or both is detected at highlevels in a vesicle from a subject suffering from NSCLC. The subject maythen be classified as a non-responder to the agents Cisplatin andCarboplatin, or the agents are considered to be less effective thanother agents for treating NSCLC in the subject and not selected for usein treating the subject. Any of the following biomarkers can be assessedin a vesicle obtained from a subject, and the biomarker can be in theform including but not limited to one or more of a nucleic acid,polypeptide, peptide or peptide mimetic. In yet another illustrativeexample, a mutation in one or more of KRAS, BRAF, PIK3CA, and/or c-kitcan be used to select a candidate treatment. For example, a mutation inKRAS or BRAF in a patient may indicate that cetuximab and/or panitumumabare likely to be less effective in treating the patient.

TABLE 9 Examples of Biomarkers, Lineage and Agents Possibly LessEffective Possible Agents to Biomarker Lineage Agents Consider AR (highexpression) Prostate Bicalutamide, Flutamide, Leuprolide, Goserelin AR(high expression) default Bicaluamide, Flutamide, Leuprolide, GoserelinBCRP (high Non-small cell lung cancer Cisplatin, Carboplatin expression)(NSCLC) BCRP (low Non-small cell lung cancer Cisplatin, Carboplatinexpression) (NSCLC) BCRP (high default Cisplatin, Carboplatinexpression) BCRP (low default Cisplatin, Carboplatin expression) BRAFV600E Colorectal Cetuximab, Panitumumab (mutation positive) BRAF V600EColorectal Cetuximab, Panitumumab (mutation negative) BRAF V600E Allother Cetuximab, Panitumumab (mutation positive) BRAF V600E All otherCetuximab, Panitumumab (mutation negative) BRAF V600E default Cetuximab,Panitumumab (mutation positive) BRAF V600E default Cetuximab,Panitumumab (mutation negative) CD52 (high Leukemia Alemtuzumabexpression) CD52 (low Leukemia Alemtuzumab expression) CD52 (highdefault (Hematologic Alemtuzumab expression) malignancies only) CD52(low default (Hematologic Alemtuzumab expression) malignancies only)c-kit Uveal Melanoma c-kit (high expression) Gastrointestinal StromalImatinib Tumors [GIST]; cKIT will not be performed on Uveal Melanoma asimatinib is not useful in the setting of WT cKIT positive uveal melanoma(see Hofmann et al. 2009) c-kit (high expression) Extrahepatic Bile DuctImatinib Tumors; cKIT will not be performed on Uveal Melanoma asimatinib is not useful in the setting of WT cKIT positive uveal melanoma(see Hofmann et al. 2009) c-kit (high expression) Acute myeloid leukemiaImatinib (AML) c-kit (high expression) default; cKIT will not beImatinib performed on Uveal Melanoma as imatinib is not useful in thesetting of WT cKIT positive uveal melanoma (see Hofmann et al. 2009)EGFR (high copy Head and neck squamous Erlotinib, Gefitinib number) cellcarcinoma (HNSCC) EGFR Head and neck squamous Erlotinib, Gefitinib cellcarcinoma (HNSCC) EGFR (high copy Non-small cell lung cancer Erlotinib,Gefitinib number) (NSCLC) EGFR (low copy Non-small cell lung cancerErlotinib, Gefitinib number) (NSCLC) EGFR (high copy default Cetuxumab,Panitumumab, number) Erlotinib, Gefitinib EGFR (low copy defaultCetuxumab, Panitumumab, number) Erlotinib, Gefitinib ER (highexpression) Breast Ixabepilone Tamoxifen-based treatment, aromataseinhibitors (anastrazole, letrozole) ER (low expression) BreastIxabepilone ER (high expression) Ovarian Tamoxifen-based treatment,aromatase inhibitors (anastrazole, letrozole) ER (high expression)default Tamoxifen-based treatment, aromatase inhibitors (anastrazole,letrozole) ERCC1 (high Non-small cell lung cancer Carboplatin, Cisplatinexpression) (NSCLC) ERCC1 (low Non-small cell lung cancer Carboplatin,Cisplatin expression) (NSCLC) ERCC1 (high Small Cell Lung CancerCarboplatin, Cisplatin expression) (SCLC) ERCC1 (low Small Cell LungCancer Carboplatin, Cisplatin expression) (SCLC) ERCC1 (high GastricOxaliplatin expression) ERCC1 (low Gastric Oxaliplatin expression) ERCC1(high default Carboplatin, Cisplatin, expression) Oxaliplatin ERCC1 (lowdefault Carboplatin, Cisplatin, expression) Oxaliplatin HER-2 (highBreast Lapatinib, Trastuzumab expression) HER-2 (high default Lapatinib,Trastuzumab expression) KRAS (mutation Colorectal cancer Cetuximab,Panitumumab positive) KRAS (mutation Colorectal cancer Cetuximab,Panitumumab negative) KRAS (mutation Non-small cell lung cancerErlotinib, Gefitinib positive) (NSCLC) KRAS (mutation Non-small celllung cancer Erlotinib, Gefitinib negative) (NSCLC) KRAS (mutationBronchioloalveolar Erlotinib positive) carcinoma (BAC) or adenocarcinoma(BAC subtype) KRAS (mutation Bronchioloalveolar Erlotinib negative)carcinoma (BAC) or adenocarcinoma (BAC subtype) KRAS (mutation Multiplemyeloma VBMCP/Cyclophosphamide positive) KRAS (mutation Multiple myelomaVBMCP/Cyclophosphamide negative) KRAS (mutation default Cetuximab,Panitumumab positive) KRAS (mutation default Cetuximab, panitumumabnegative) KRAS (mutation default Cetuximab, Erlotinib, positive)Panitumumab, Gefitinib KRAS (mutation default Cetuximab, Erlotinib,negative) Panitumumab, Gefitinib MGMT (high Pituitary tumors,Temozolomide expression) oligodendroglioma MGMT (low Pituitary tumors,Temozolomide expression) oligodendroglioma MGMT (high Neuroendocrinetumors Temozolomide expression) MGMT (low Neuroendocrine tumorsTemozolomide expression) MGMT (high default Temozolomide expression)MGMT (low default Temozolomide expression) MRP1 (high BreastCyclophosphamide expression) MRP1 (low Breast Cyclophosphamideexpression) MRP1 (high Small Cell Lung Cancer Etoposide expression)(SCLC) MRP1 (low Small Cell Lung Cancer Etoposide expression) (SCLC)MRP1 (high Nodal Diffuse Large B- Cyclophosphamide/Vincristineexpression) Cell Lymphoma MRP1 (low Nodal Diffuse Large B-Cyclophosphamide/Vincristine expression) Cell Lymphoma MRP1 (highdefault Cyclophosphamide, expression) Etoposide, Vincristine MRP1 (lowdefault Cyclophosphamide, expression) Etoposide, Vincristine PDGFRA(high Malignant Solitary Fibrous Imatinib expression) Tumor of thePleura (MSFT) PDGFRA (high Gastrointestinal stromal Imatinib expression)tumor (GIST) PDGFRA (high Default Imatinib expression) p-glycoprotein(high Acute myeloid leukemia Etoposide expression) (AML) p-glycoprotein(low Acute myeloid leukemia Etoposide expression) (AML) p-glycoprotein(high Diffuse Large B-cell Doxorubicin expression) Lymphoma (DLBCL)p-glycoprotein (low Diffuse Large B-cell Doxorubicin expression)Lymphoma (DLBCL) p-glycoprotein (high Lung Etoposide expression)p-glycoprotein (low Lung Etoposide expression) p-glycoprotein (highBreast Doxorubicin expression) p-glycoprotein (low Breast Doxorubicinexpression) p-glycoprotein (high Ovarian Paclitaxel expression)p-glycoprotein (low Ovarian Paclitaxel expression) p-glycoprotein (highHead and neck squamous Vincristine expression) cell carcinoma (HNSCC)p-glycoprotein (low Head and neck squamous Vincristine expression) cellcarcinoma (HNSCC) p-glycoprotein (high default Vincristine, Etoposide,expression) Doxorubicin, Paclitaxel p-glycoprotein (low defaultVincristine, Etoposide, expression) Doxorubicin, Paclitaxel PR (highexpression) Breast Chemoendocrine therapy Tamoxifen, Anastrazole,Letrozole PR (low expression) default Chemoendocrine therapy Tamoxifen,Anastrazole, Letrozole PTEN (high Breast Trastuzumab expression) PTEN(low Breast Trastuzumab expression) PTEN (high Non-small cell LungGefitinib expression) Cancer (NSCLC) PTEN (low Non-small cell LungGefitinib expression) Cancer (NSCLC) PTEN (high Colorectal Cetuximab,Panitumumab expression) PTEN (low Colorectal Cetuximab, Panitumumabexpression) PTEN (high Glioblastoma Erlotinib, Gefitinib expression)PTEN (low Glioblastoma Erlotinib, Gefitinib expression) PTEN (highdefault Cetuximab, Panitumumab, expression) Erlotinib, Gefitinib andTrastuzumab PTEN (low default Cetuximab, Panitumumab, expression)Erlotinib, Gefitinib and Trastuzumab RRM1 (high Non-small cell lungcancer Gemcitabine experssion) (NSCLC) RRM1 (low Non-small cell lungcancer Gemcitabine expression) (NSCLC) RRM1 (high Pancreas Gemcitabineexperssion) RRM1 (low Pancreas Gemcitabine expression) RRM1 (highdefault Gemcitabine experssion) RRM1 (low default Gemcitabineexpression) SPARC (high Breast nab-paclitaxel expression) SPARC (highdefault nab-paclitaxel expression) TS (high expression) Colorectalfluoropyrimidines TS (low expression) Colorectal fluoropyrimidines TS(high expression) Pancreas fluoropyrimidines TS (low expression)Pancreas fluoropyrimidines TS (high expression) Head and Neck Cancerfluoropyrimidines TS (low expression) Head and Neck Cancerfluoropyrimidines TS (high expression) Gastric fluoropyrimidines TS (lowexpression) Gastric fluoropyrimidines TS (high expression) Non-smallcell lung cancer fluoropyrimidines (NSCLC) TS (low expression) Non-smallcell lung cancer fluoropyrimidines (NSCLC) TS (high expression) Liverfluoropyrimidines TS (low expression) Liver fluoropyrimidines TS (highexpression) default fluoropyrimidines TS (low expression) defaultfluoropyrimidines TOPO1 (high Colorectal Irinotecan expression) TOPO1(low Colorectal Irinotecan expression) TOPO1 (high Ovarian Irinotecanexpression) TOPO1 (low Ovarian Irinotecan expression) TOPO1 (highdefault Irinotecan expression) TOPO1 (low default Irinotecan expression)TopoIIa (high Breast Doxorubicin, liposomal- epxression) Doxorubicin,Epirubicin TopoIIa (low Breast Doxorubicin, liposomal- expression)Doxorubicin, Epirubicin TopoIIa (high default Doxorubicin, liposomal-epxression) Doxorubicin, Epirubicin TopoIIa (low default Doxorubicin,liposomal- expression) Doxorubicin, Epirubicin

Other examples of biomarkers that can be detected and the treatmentagents that can be selected or possibly avoided based on the biomarkersignatures are listed in Table 10. For example, for a subject sufferingfrom cancer, detecting overexpression of ADA in vesicles from a subjectis used to classify the subject as a responder to pentostatin, orpentostatin identified as an agent to use for treating the subject. Inanother example, for a subject suffering from cancer, detectingoverexpression of BCRP in vesicles from the subject is used to classifythe subject as a non-responder to cisplatin, carboplatin, irinotecan,and topotecan, meaning that cisplatin, carboplatin, irinotecan, andtopotecan are identified as agents that are suboptimal for treating thesubject.

TABLE 10 Examples of Biomarkers, Agents and Resistance Gene NameExpression Status Candidate Agent(s) Possible Resistance ADAOverexpressed pentostatin ADA Underexpressed cytarabine AR Overexpressedabarelix, bicalutamide, flutamide, gonadorelin, goserelin, leuprolideASNS Underexpressed asparaginase, pegaspargase BCRP (ABCG2)Overexpressed cisplatin, carboplatin, irinotecan, topotecan BRCA1Underexpressed mitomycin BRCA2 Underexpressed mitomycin CD52Overexpressed alemtuzumab CDA Overexpressed cytarabine c-erbB2 Highlevels of Trastuzumab, c-erbB2 phosphorylation in kinase inhibitor,lapatinib epithelial cells CES2 Overexpressed irinotecan c-kitOverexpressed sorafenib, sunitinib, imatinib COX-2 Overexpressedcelecoxib DCK Overexpressed gemcitabine cytarabine DHFR Underexpressedmethotrexate, pemetrexed DHFR Overexpressed methotrexate DNMT1Overexpressed azacitidine, decitabine DNMT3A Overexpressed azacitidine,decitabine DNMT3B Overexpressed azacitidine, decitabine EGFROverexpressed erlotinib, gefitinib, cetuximab, panitumumab EML4-ALKOverexpressed (present) crizotinib EPHA2 Overexpressed dasatinib EROverexpressed anastrazole, exemestane, fulvestrant, letrozole,megestrol, tamoxifen, medroxyprogesterone, toremifene, aminoglutethimideERCC1 Overexpressed carboplatin, cisplatin GART Underexpressedpemetrexed GRN (PCDGF, PGRN) Overexpressed anti-oestrogen therapy,tamoxifen, faslodex, letrozole, herceptin in Her-2 overexpressing cells,doxorubicin HER-2 (ERBB2) Overexpressed trastuzumab, lapatinib HIF-1αOverexpressed sorafenib, sunitinib, bevacizumab IκB-α Overexpressedbortezomib MGMT Underexpressed temozolomide MGMT Overexpressedtemozolomide MRP1 (ABCC1) Overexpressed etoposide, paclitaxel,docetaxel, vinblastine, vinorelbine, topotecan, teniposide P-gp (ABCB1)Overexpressed doxorubicin, etoposide, epirubicin, paclitaxel, docetaxel,vinblastine, vinorelbine, topotecan, teniposide, liposomal doxorubicinPDGFR-α Overexpressed sorafenib, sunitinib, imatinib PDGFR-βOverexpressed sorafenib, sunitinib, imatinib PR Overexpressedexemestane, fulvestrant, gonadorelin, goserelin, medroxyprogesterone,megestrol, tamoxifen, toremifene RARA Overexpressed ATRA RRM1Underexpressed gemcitabine, hydroxyurea RRM2 Underexpressed gemcitabine,hydroxyurea RRM2B Underexpressed gemcitabine, hydroxyurea RXR-αOverexpressed bexarotene RXR-β Overexpressed bexarotene SPARCOverexpressed nab-paclitaxel SRC Overexpressed dasatinib SSTR2Overexpressed octreotide SSTR5 Overexpressed octreotide TOPO IOverexpressed irinotecan, topotecan TOPO IIα Overexpressed doxorubicin,epirubicin, liposomal-doxorubicin TOPO IIβ Overexpressed doxorubicin,epirubicin, liposomal-doxorubicin TS Underexpressed capecitabine, 5-fluorouracil, pemetrexed TS Overexpressed capecitabine, 5- fluorouracilVDR Overexpressed calcitriol, cholecalciferol VEGFR1 (Flt1)Overexpressed sorafenib, sunitinib, bevacizumab VEGFR2 Overexpressedsorafenib, sunitinib, bevacizumab VHL Underexpressed sorafenib,sunitinib

Further drug associations and rules that are used in embodiments of theinvention are found in U.S. patent application Ser. No. 12/658,770,filed Feb. 12, 2010; International PCT Patent ApplicationPCT/US2010/000407, filed Feb. 11, 2010; International PCT PatentApplication PCT/US2010/54366, filed Oct. 27, 2010; and U.S. ProvisionalPatent Application 61/427,788, filed Dec. 28, 2010; all of whichapplications are incorporated by reference herein in their entirety.See, e.g., “Table 4: Rules Summary for Treatment Selection” ofPCT/US2010/54366.

Any drug-associated target can be part of a biosignature for providing atheranosis. A “druggable target” comprising a target that can bemodulated with a therapeutic agent such as a small molecule or biologic,is a candidate for inclusion in the biosignature of the invention.Drug-associated targets also include biomarkers that can conferresistance to a treatment, such as shown in Tables 9 and 10. Thebiosignature can be based on either the gene, e.g., DNA sequence, and/orgene product, e.g., mRNA or protein, or the drug-associated target. Suchnucleic acid and/or polypeptide can be profiled as applicable as topresence or absence, level or amount, activity, mutation, sequence,haplotype, rearrangement, copy number, or other measurablecharacteristic. The gene or gene product can be associated with avesicle population, e.g., as a vesicle surface marker or as vesiclepayload. In an embodiment, the invention provides a method oftheranosing a cancer, comprising identifying a biosignature thatcomprises a presence or level of one or more drug-associated target, andselecting a candidate therapeutic based on the biosignature. Thedrug-associated target can be a circulating biomarker, a vesicle, or avesicle associated biomarker. Because drug-associated targets can beindependent of the tissue or cell-of-origin, biosignatures comprisingdrug-associated targets can be used to provide a theranosis for anyproliferative disease, such as cancers from various anatomical origins,including cancers of unknown origin such as CUPS.

The drug-associated targets assessed using the methods of the inventioncomprise without limitation ABCC1, ABCG2, ACE2, ADA, ADH1C, ADH4, AGT,AR, AREG, ASNS, BCL2, BCRP, BDCA1, beta III tubulin, BIRC5, B-RAF,BRCA1, BRCA2, CA2, caveolin, CD20, CD25, CD33, CD52, CDA, CDKN2A,CDKN1A, CDKN1B, CDK2, CDW52, CES2, CK 14, CK 17, CK 5/6, c-KIT, c-Met,c-Myc, COX-2, Cyclin D1, DCK, DHFR, DNMT1, DNMT3A, DNMT3B, E-Cadherin,ECGF1, EGFR, EML4-ALK fusion, EPHA2, Epiregulin, ER, ERBR2, ERCC1,ERCC3, EREG, ESR1, FLT1, folate receptor, FOLR1, FOLR2, FSHB, FSHPRH1,FSHR, FYN, GART, GNA11, GNAQ, GNRH1, GNRHR1, GSTP1, HCK, HDAC1, hENT-1,Her2/Neu, HGF, HIF1A, HIG1, HSP90, HSP90AA1, HSPCA, IGF-1R, IGFRBP,IGFRBP3, IGFRBP4, IGFRBP5, IL13RA1, IL2RA, KDR, Ki67, KIT, K-RAS, LCK,LTB, Lymphotoxin Beta Receptor, LYN, MET, MGMT, MLH1, MMR, MRP1, MS4A1,MSH2, MSH5, Myc, NFKB1, NFKB2, NFKBIA, NRAS, ODC1, OGFR, p16, p21, p27,p53, p95, PARP-1, PDGFC, PDGFR, PDGFRA, PDGFRB, PGP, PGR, PI3K, POLA,POLA1, PPARG, PPARGC1, PR, PTEN, PTGS2, PTPN12, RAF1, RARA, ROS1, RRM1,RRM2, RRM2B, RXRB, RXRG, SIK2, SPARC, SRC, SSTR1, SSTR2, SSTR3, SSTR4,SSTR5, Survivin, TK1, TLE3, TNF, TOP1, TOP2A, TOP2B, TS, TUBB3, TXN,TXNRD1, TYMS, VDR, VEGF, VEGFA, VEGFC, VHL, YES1, ZAP70, or anycombination thereof. A biosignature including one or combination ofthese markers can be used to characterize a phenotype according to theinvention, such as providing a theranosis. These markers are known toplay a role in the efficacy of various chemotherapeutic agents againstproliferative diseases. Accordingly, the markers can be assessed toselect a candidate treatment for the cancer independent of the origin ortype of cancer. In an embodiment, the invention provides a method ofselecting a candidate therapeutic for a cancer, comprising identifying abiosignature comprising a level or presence of one or more drugassociated target, and selecting the candidate therapeutic based on itspredicted efficacy for a patient with the biosignature. The one or moredrug-associated target can be one of the targets listed above, or inTables 9-10. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10,12, 15, 20, 25, 30, 35, 40, 45, or at least 50 of the one or moredrug-associated targets are assessed. The one or more drug-associatedtarget can be associated with a vesicle, e.g., as a vesicle surfacemarker or as vesicle payload as either nucleic acid (e.g., DNA, mRNA) orprotein. In some embodiments, the presence or level of a microRNA knownto interact with the one or more drug-associated target is assessed,wherein a high level of microRNA known to suppress the one or moredrug-associated target can indicate a lower expression of the one ormore drug-associated target and thus a lower likelihood of response to atreatment against the drug-associated target. The one or moredrug-associated target can be circulating biomarkers. The one or moredrug-associated target can be assessed in a tissue sample. The predictedefficacy can be determined by comparing the presence or level of the oneor more drug-associated target to a reference value, wherein a higherlevel that the reference indicates that the subject is a likelyresponder. The predicted efficacy can be determined using a classifieralgorithm, wherein the classifier was trained by comparing thebiosignature of the one or more drug-associated target in subjects thatare known to be responders or non-responders to the candidate treatment.Molecular associations of the one or more drug-associated target withappropriate candidate targets are displayed in Tables 9-10 herein andU.S. patent application Ser. No. 12/658,770, filed Feb. 12, 2010;International PCT Patent Application PCT/US2010/000407, filed Feb. 11,2010; International PCT Patent Application PCT/US2010/54366, filed Oct.27, 2010; International Patent Application Serial No. PCT/US2011/031479,entitled “Circulating Biomarkers for Disease” and filed Apr. 6, 2011;and U.S. Provisional Patent Application 61/427,788, filed Dec. 28, 2010;all of which applications are incorporated by reference herein in theirentirety.

Table 11 of International Patent Application Serial No.PCT/US2011/031479, provides a listing of gene and corresponding proteinsymbols and names of many of the theranostic targets that are analyzedaccording to the methods of the invention. As understood by those ofskill in the art, genes and proteins have developed a number ofalternative names in the scientific literature. Thus, the listing inTable 11 of PCT/US2011/031479 comprises an illustrative but notexhaustive compilation. A further listing of gene aliases anddescriptions can be found using a variety of online databases, includingGeneCards® (www.genecards.org), HUGO Gene Nomenclature(www.genenames.org), Entrez Gene(www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene), UniProtKB/Swiss-Prot(www.uniprot.org), UniProtKB/TrEMBL (www.uniprot.org), OMIM(www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM), GeneLoc(genecards.weizmann.ac.il/geneloc/), and Ensembl (www.ensembl.org).Generally, gene symbols and names below correspond to those approved byHUGO, and protein names are those recommended by UniProtKB/Swiss-Prot.Common alternatives are provided as well. Where a protein name indicatesa precursor, the mature protein is also implied. Throughout theapplication, gene and protein symbols may be used interchangeably andthe meaning can be derived from context as necessary.

As an illustration, a treatment can be selected for a subject sufferingfrom Non-Small Cell Lung Cancer. One or more biomarkers, such as, butnot limited to, EGFR, excision repair cross-complementation group 1(ERCC1), p53, Ras, p27, class III beta tubulin, breast cancer gene 1(BRCA1), breast cancer gene 1 (BRCA2), and ribonucleotide reductasemessenger 1 (RRM1), can be assessed from a vesicle from the subject.Based on one or more characteristics of the one or more biomarkers, thesubject can be determined to be a responder or non-responder for atreatment, such as, but not limited to, Erlotinib, Carboplatin,Paclitaxel, Gefitinib, or a combination thereof.

In another embodiment, a treatment can be selected for a subjectsuffering from Colorectal Cancer, and a biomarker, such as, but notlimited to, K-ras, can be assessed from a vesicle from the subject.Based on one or more characteristics of the one or more biomarkers, thesubject can be determined to be a responder or non-responder for atreatment, such as, but not limited to, Panitumumab, Cetuximab, or acombination thereof.

In another embodiment, a treatment can be selected for a subjectsuffering from Breast Cancer. One or more biomarkers, such as, but notlimited to, HER2, toposiomerase II α, estrogen receptor, andprogesterone receptor, can be assessed from a vesicle from the subject.Based on one or more characteristics of the one or more biomarkers, thesubject can be determined to be a responder or non-responder for atreatment, such as, but not limited to, trastuzumab, anthracyclines,taxane, methotrexate, fluorouracil, or a combination thereof.

As described, the biosignature used to theranose a cancer can compriseanalysis of one or more biomarker, which can be a protein or nucleicacid, including a mRNA or a microRNA. The biomarker can be detected in abodily fluid and/or can be detected associated with a vesicle, e.g., asa vesicle antigen or as vesicle payload. In an illustrative example, thebiosignature is used to identify a patient as a responder ornon-responder to a tyrosine kinase inhibitor. The biomarkers can be oneor more of those described in WO/2010/121238, entitled “METHODS AND KITSTO PREDICT THERAPEUTIC OUTCOME OF TYROSINE KINASE INHIBITORS” and filedApr. 19, 2010; or WO/2009/105223, entitled “SYSTEMS AND METHODS OFCANCER STAGING AND TREATMENT” and filed Feb. 19, 2009; both of whichapplications are incorporated herein by reference in their entirety.

In an aspect, the present invention provides a method of determiningwhether a subject is likely to respond or not to a tyrosine kinaseinhibitor, the method comprising identifying one or more biomarker in avesicle population in a sample from the subject, wherein differentialexpression of the one or more biomarker in the sample as compared to areference indicates that the subject is a responder or non-responder tothe tyrosine kinase inhibitor. In an embodiment, the one or morebiomarker comprises miR-497, wherein reduced expression of miR-497indicates that the subject is a responder (i.e., sensitive to thetyrosine kinase inhibitor). In another embodiment, the one or morebiomarker comprises one or more of miR-21, miR-23a, miR-23b, andmiR-29b, wherein upregulation of the microRNA indicates that the subjectis a likely non-responder (i.e., resistant to the tyrosine kinaseinhibitor). In some embodiments, the one or more biomarker comprises oneor more of hsa-miR-029a, hsa-let-7d, hsa-miR-100, hsa-miR-1260,hsa-miR-025, hsa-let-71, hsa-miR-146a, hsa-miR-594-Pre, hsa-miR-024,FGFR1, MET, RAB25, EGFR, KIT and VEGFR2. In another embodiment, the oneor more biomarker comprises FGF1, HOXC10 or LHFP, wherein higherexpression of the biomarker indicates that the subject is anon-responder (i.e., resistant to the tyrosine kinase inhibitor). Themethod can be used to determine the sensitivity of a cancer to thetyrosine kinase inhibitor, e.g., a non-small cell lung cancer cell,kidney cancer or GIST. The tyrosine kinase inhibitor can be erlotinib,vandetanib, sunitinib and/or sorafenib, or other inhibitors that operateby a similar mechanism of action. A tyrosine kinase inhibitor includesany agent that inhibits the action of one or more tyrosine kinases in aspecific or non-specific fashion. Tyrosine kinase inhibitors includesmall molecules, antibodies, peptides, or any appropriate entity thatdirectly, indirectly, allosterically, or in any other way inhibitstyrosine residue phosphorylation. Specific examples of tyrosine kinaseinhibitors includeN-(trifluoromethylphenyl)-5-methylisoxazol-4-carboxamide,3-[(2,4-dimethylpyrrol-5-yl)methylidenyl)indolin-2-one,17-(allylamino)-17-demethoxygeldanamycin,4-(3-chloro-4-fluorophenylamino)-7-methoxy-643-(4-morpholinyl)propoxyl]q-uinazoline,N-(3-ethynylphenyl)-6,7-bis(2-methoxyethoxy)-4-quinazolinamine,BIBX1382,2,3,9,10,11,12-hexahydro-10-(hydroxymethyl)-10-hydroxy-9-methyl-9,12-epox-y-1H-d{umlautover(ν)}ndolo[1,2,3-fg:3′,2′,1′-kl]pyrrolo[3,4-i][1,6]benzodiazocin-1-one,SH268, genistein, STI571, CEP2563,4-(3-chlorophenylamino)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidinemethanesulfonate, 4-(3-bromo-4-hydroxyphenyl)amino-6,7-dimethoxyquinazoline,4-(4′-hydroxyphenyl)amino-6,7-dimethoxyquinazoline, SU6668, STI571A,N-4-chlorophenyl-4-(4-pyridylmethyl)-1-phthalazinamine,N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-1,2-dihydro-2-oxo-3H-indol-3-ylidine)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide(commonly known as sunitinib), A-[A-[[4-chloro-3(trifluoromethyl)phenyl]carbamoylamino]phenoxy]-N-methyl-pyridine-2-carboxamide(commonly known as sorafenib), EMD121974, andN-(3-ethynylphenyl)-6,7-bis(2-methoxyethoxy)quinazolin-4-amine (commonlyknown as erlotinib). In some embodiments, the tyrosine kinase inhibitorhas inhibitory activity upon the epidermal growth factor receptor(EGFR), VEGFR, PDGFR beta, and/or FLT3.

Thus, a treatment can be selected for the subject suffering from acancer, based on a biosignature identified by the methods of theinvention. Accordingly, the biosignature can comprise a presence orlevel of a circulating biomarker, including a microRNA, a vesicle, orany useful vesicle associated biomarker.

Biomarkers that can be used for theranosis of other diseases using themethods of the invention, including cardiovascular disease, neurologicaldiseases and disorders, immune diseases and disorders and infectiousdisease, are described in International Patent Application Serial No.PCT/US2011/031479, entitled “Circulating Biomarkers for Disease” andfiled Apr. 6, 2011, which application is incorporated by reference inits entirety herein.

Biosignature Discovery

The systems and methods provided herein can be used in identifying anovel biosignature of a vesicle, such as one or more novel biomarkersfor the diagnosis, prognosis or theranosis of a phenotype. In oneembodiment, one or more vesicles can be isolated from a subject with aphenotype and a biosignature of the one or more vesicles determined. Thebiosignature can be compared to a subject without the phenotype.Differences between the two biosignatures can be determined and used toform a novel biosignature. The novel biosignature can then be used foridentifying another subject as having the phenotype or not having thephenotype.

Differences between the biosignature from a subject with a particularphenotype can be compared to the biosignature from a subject without theparticular phenotype. The one or more differences can be a difference inany characteristic of the vesicle. For example, the level or amount ofvesicles in the sample, the half-life of the vesicle, the circulatinghalf-life of the vesicle, the metabolic half-life of the vesicle, or theactivity of the vesicle, or any combination thereof, can differ betweenthe biosignature from the subject with a particular phenotype and thebiosignature from the subject without the particular phenotype.

In some embodiments, one or more biomarkers differ between thebiosignature from the subject with a particular phenotype and thebiosignature from the subject without the particular phenotype. Forexample, the expression level, presence, absence, mutation, variant,copy number variation, truncation, duplication, modification, molecularassociation of one or more biomarkers, or any combination thereof, maydiffer between the biosignature from the subject with a particularphenotype and the biosignature from the subject without the particularphenotype. The biomarker can be any biomarker disclosed herein or thatcan be used to characterize a biological entity, including a circulatingbiomarker, such as protein or microRNA, a vesicle, or a componentpresent in a vesicle or on the vesicle, such as any nucleic acid (e.g.RNA or DNA), protein, peptide, polypeptide, antigen, lipid,carbohydrate, or proteoglycan.

In an aspect, the invention provides a method of discovering a novelbiosignature comprising comparing the biomarkers between two or moresample groups to identify biomarkers that show a difference between thesample groups. Multiple markers can be assessed in a panel format topotentially improve the performance of individual markers. In someembodiments, the multiple markers are assessed in a multiplex fashion.The ability of the individual markers and groups of markers todistinguish the groups can be assessed using statistical discriminateanalysis or classification methods as used herein. Optimal panels ofmarkers can be used as a biosignature to characterize the phenotypeunder analysis, such as to provide a diagnosis, prognosis or theranosisof a disease or condition. Optimization can be based on variouscriteria, including without limitation maximizing ROC AUC, accuracy,sensitivity at a certain specificity, or specificity at a certainsensitivity. The panels can include biomarkers from multiple types. Forexample, the biosignature can comprise vesicle antigens useful forcapturing a vesicle population of interest, and the biosignature canfurther comprise payload markers within the vesicle population,including without limitation microRNAs, mRNAs, or soluble proteins.Optimal combinations can be identified as those vesicle antigens andpayload markers with the greatest ROC AUC value when comparing twosettings. As another example, the biosignature can be determined byassessing a vesicle population in addition to assessing circulatingbiomarkers that are not obtained by isolating exosomes, such ascirculating proteins and/or microRNAs.

The phenotype can be any of those listed herein, e.g., in the“Phenotype” section above. For example, the phenotype can be aproliferative disorder such as a cancer or non-malignant growth, aperinatal or pregnancy related condition, an infectious disease, aneurological disorder, a cardiovascular disease, an inflammatorydisease, an immune disease, or an autoimmune disease. The cancerincludes without limitation lung cancer, non-small cell lung cancer,small cell lung cancer (including small cell carcinoma (oat cellcancer), mixed small cell/large cell carcinoma, and combined small cellcarcinoma), colon cancer, breast cancer, prostate cancer, liver cancer,pancreatic cancer, brain cancer, kidney cancer, ovarian cancer, stomachcancer, melanoma, bone cancer, gastric cancer, breast cancer, glioma,glioblastoma, hepatocellular carcinoma, papillary renal carcinoma, headand neck squamous cell carcinoma, leukemia, lymphoma, myeloma, or othersolid tumors.

Any of the types of biomarkers or specific biomarkers described hereincan be assessed to discover a novel biosignature, e.g., the biomarkersin Tables 3-5. In an embodiment, the biomarkers selected for discoverycomprise cell-specific biomarkers as listed herein, including withoutlimitation the genes and microRNA listed in FIGS. 1-60 of InternationalPatent Application Serial No. PCT/US2011/031479, entitled “CirculatingBiomarkers for Disease” and filed Apr. 6, 2011, which application isincorporated by reference in its entirety herein, Tables 9-10 or Table16. The biomarkers can comprise one or more disease associated, drugassociated, or prognostic target such as listed in Table 11. Thebiomarkers can comprise one or more general vesicle marker, one or morecell-specific vesicle marker, and/or one or more disease-specificvesicle marker.

TABLE 11 Disease- and Drug-associated Biomarkers Gene Protein SymbolGene Name Symbol Protein Name ABCB1, PGP ATP-binding cassette,sub-family B ABCB1, Multidrug resistance protein 1; P- (MDR/TAP), member1 MDR1, PGP glycoprotein ABCC1, ATP-binding cassette, sub-family C MRP1,Multidrug resistance-associated protein 1 MRP1 (CFTR/MRP), member 1ABCC1 ABCG2, ATP-binding cassette, sub-family G ABCG2 ATP-bindingcassette sub-family G member 2 BCRP (WHITE), member 2 ACE2 angiotensin Iconverting enzyme ACE2 Angiotensin-converting enzyme 2 precursor(peptidyl-dipeptidase A) 2 ADA adenosine deaminase ADA Adenosinedeaminase ADH1C alcohol dehydrogenase 1C (class I), ADH1G Alcoholdehydrogenase 1C gamma polypeptide ADH4 alcohol dehydrogenase 4 (classII), pi ADH4 Alcohol dehydrogenase 4 polypeptide AGT angiotensinogen(serpin peptidase ANGT, AGT Angiotensinogen precursor inhibitor, cladeA, member 8) ALK anaplastic lymphoma receptor tyrosine ALK ALK tyrosinekinase receptor precursor kinase AR androgen receptor AR Androgenreceptor AREG amphiregulin AREG Amphiregulin precursor ASNS asparaginesynthetase ASNS Asparagine synthetase [glutamine- hydrolyzing] BCL2B-cell CLL/lymphoma 2 BCL2 Apoptosis regulator Bcl-2 BDCA1, CD1cmolecule CD1C T-cell surface glycoprotein CD1c precursor CD1C BIRC5baculoviral IAP repeat-containing 5 BIRC5, Baculoviral IAPrepeat-containing protein 5; Survivin Survivin BRAF v-raf murine sarcomaviral oncogene B-RAF, Serine/threonine-protein kinase B-raf homolog B1BRAF BRCA1 breast cancer 1, early onset BRCA1 Breast cancer type 1susceptibility protein BRCA2 breast cancer 2, early onset BRCA2 Breastcancer type 2 susceptibility protein CA2 carbonic anhydrase II CA2Carbonic anhydrase 2 CAV1 caveolin 1, caveolae protein, 22 kDa CAV1Caveolin-1 CCND1 cyclin D1 CCND1, G1/S-specific cyclin-D1 Cyclin D1,BCL-1 CD20, membrane-spanning 4-domains, CD20 B-lymphocyte antigen CD20MS4A1 subfamily A, member 1 CD25, interleukin 2 receptor, alpha CD25Interleukin-2 receptor subunit alpha IL2RA precursor CD33 CD33 moleculeCD33 Myeloid cell surface antigen CD33 precursor CD52, CD52 moleculeCD52 CAMPATH-1 antigen precursor CDW52 CDA cytidine deaminase CDACytidine deaminase CDH1, cadherin 1, type 1, E-cadherin E-Cad Cadherin-1precursor (E-cadherin) ECAD (epithelial) CDK2 cyclin-dependent kinase 2CDK2 Cell division protein kinase 2 CDKN1A, cyclin-dependent kinaseinhibitor 1A CDKN1A, Cyclin-dependent kinase inhibitor 1 P21 (p21, Cip1)p21 CDKN1B cyclin-dependent kinase inhibitor 1B CDKN1B, Cyclin-dependentkinase inhibitor 1B (p27, Kip1) p27 CDKN2A, cyclin-dependent kinaseinhibitor 2A CD21A, p16 Cyclin-dependent kinase inhibitor 2A, P16(melanoma, p16, inhibits CDK4) isoforms 1/2/3 CES2 carboxylesterase 2(intestine, liver) CES2, EST2 Carboxylesterase 2 precursor CK 5/6cytokeratin 5/cytokeratin 6 CK 5/6 Keratin, type II cytoskeletal 5;Keratin, type II cytoskeletal 6 CK14, keratin 14 CK14 Keratin, type Icytoskeletal 14 KRT14 CK17, keratin 17 CK17 Keratin, type I cytoskeletal17 KRT17 COX2, prostaglandin-endoperoxide synthase 2 COX-2,Prostaglandin G/H synthase 2 precursor PTGS2 (prostaglandin G/H synthaseand PTGS2 cyclooxygenase) DCK deoxycytidine kinase DCK Deoxycytidinekinase DHFR dihydrofolate reductase DHFR Dihydrofolate reductase DNMT1DNA (cytosine-5-)-methyltransferase 1 DNMT1 DNA(cytosine-5)-methyltransferase 1 DNMT3A DNA(cytosine-5-)-methyltransferase 3 DNMT3A DNA(cytosine-5)-methyltransferase 3A alpha DNMT3B DNA(cytosine-5-)-methyltransferase 3 DNMT3B DNA(cytosine-5)-methyltransferase 3B beta ECGF1, thymidine phosphorylaseTYMP, PD- Thymidine phosphorylase precursor TYMP ECGF, ECDF1 EGFR,epidermal growth factor receptor EGFR, Epidermal growth factor receptorprecursor ERBB1, (erythroblastic leukemia viral (v-erb-b) ERBB1, HER1oncogene homolog, avian) HER1 EML4 echinoderm microtubule associatedEML4 Echinoderm microtubule-associated protein- protein like 4 like 4EPHA2 EPH receptor A2 EPHA2 Ephrin type-A receptor 2 precursor ER, ESR1estrogen receptor 1 ER, ESR1 Estrogen receptor ERBB2, v-erb-b2erythroblastic leukemia viral ERBB2, Receptor tyrosine-protein kinaseerbB-2 HER2/NEU oncogene homolog 2, neuro/glioblastoma HER2, HER-precursor derived oncogene homolog (avian) 2/neu ERCC1 excision repaircross-complementing ERCC1 DNA excision repair protein ERCC-1 rodentrepair deficiency, complementation group 1 (includes overlappingantisense sequence) ERCC3 excision repair cross-complementing ERCC3TFIIH basal transcription factor complex rodent repair deficiency,helicase XPB subunit complementation group 3 (xeroderma pigmentosumgroup B complementing) EREG Epiregulin EREG Proepiregulin precursor FLT1fms-related tyrosine kinase 1 (vascular FLT-1, Vascular endothelialgrowth factor receptor endothelial growth factor/vascular VEGFR1 1precursor permeability factor receptor) FOLR1 folate receptor 1 (adult)FOLR1 Folate receptor alpha precursor FOLR2 folate receptor 2 (fetal)FOLR2 Folate receptor beta precursor FSHB follicle stimulating hormone,beta FSHB Follitropin subunit beta precursor polypeptide FSHPRH1,centromere protein I FSHPRH1, Centromere protein I CENP1 CENP1 FSHRfollicle stimulating hormone receptor FSHR Follicle-stimulating hormonereceptor precursor FYN FYN oncogene related to SRC, FGR, FYNTyrosine-protein kinase Fyn YES GART phosphoribosylglycinamide GART,PUR2 Trifunctional purine biosynthetic protein formyltransferase,adenosine-3 phosphoribosylglycinamide synthetase,phosphoribosylaminoimidazole synthetase GNA11, guanine nucleotidebinding protein (G GNA11, G Guanine nucleotide-binding protein subunitGA11 protein), alpha 11 (Gq class) alpha-11, G- alpha-11 protein subunitalpha- 11 GNAQ, guanine nucleotide binding protein (G GNAQ Guaninenucleotide-binding protein G(q) GAQ protein), q polypeptide subunitalpha GNRH1 gonadotropin-releasing hormone 1 GNRH1, Progonadoliberin-1precursor (luteinizing-releasing hormone) GON1 GNRHR1,gonadotropin-releasing hormone GNRHR1 Gonadotropin-releasing hormonereceptor GNRHR receptor GSTP1 glutathione S-transferase pi 1 GSTP1Glutathione S-transferase P HCK hemopoietic cell kinase HCKTyrosine-protein kinase HCK HDAC1 histone deacetylase 1 HDAC1 Histonedeacetylase 1 HGF hepatocyte growth factor (hepapoietin A; HGFHepatocyte growth factor precursor scatter factor) HIF1A hypoxiainducible factor 1, alpha subunit HIF1A Hypoxia-inducible factor 1-alpha(basic helix-loop-helix transcription factor) HIG1, HIG1 hypoxiainducible domain family, HIG1, HIG1 domain family member 1A HIGD1A,member 1A HIGD1A, HIG1A HIG1A HSP90AA1, heat shock protein 90 kDa alphaHSP90, Heat shock protein HSP 90-alpha HSP90, (cytosolic), class Amember 1 HSP90A HSPCA IGF1R insulin-like growth factor 1 receptor IGF-1RInsulin-like growth factor 1 receptor precursor IGFBP3, insulin-likegrowth factor binding protein 3 IGFBP-3, Insulin-like growthfactor-binding protein 3 IGFRBP3 IBP-3 precursor IGFBP4, insulin-likegrowth factor binding protein 4 IGFBP-4, Insulin-like growthfactor-binding protein 4 IGFRBP4 IBP-4 precursor IGFBP5, insulin-likegrowth factor binding protein 5 IGFBP-5, Insulin-like growthfactor-binding protein 5 IGFRBP5 IBP-5 precursor IL13RA1 interleukin 13receptor, alpha 1 IL-13RA1 Interleukin-13 receptor subunit alpha-1precursor KDR kinase insert domain receptor (a type III KDR, Vascularendothelial growth factor receptor receptor tyrosine kinase) VEGFR2 2precursor KIT, c-KIT v-kit Hardy-Zuckerman 4 feline sarcoma KIT, c-KIT,Mast/stem cell growth factor receptor viral oncogene homolog CD117, SCFRprecursor KRAS v-Ki-ras2 Kirsten rat sarcoma viral K-RAS GTPase KRasprecursor oncogene homolog LCK lymphocyte-specific protein tyrosine LCKTyrosine-protein kinase Lck kinase LTB lymphotoxin beta (TNFsuperfamily, LTB, TNF3 Lymphotoxin-beta member 3) LTBR lymphotoxin betareceptor (TNFR LTBR, Tumor necrosis factor receptor superfamilysuperfamily, member 3) LTBR3, member 3 precursor TNFR LYN v-yes-1Yamaguchi sarcoma viral related LYN Tyrosine-protein kinase Lyn oncogenehomolog MET, c-MET met proto-oncogene (hepatocyte growth MET, c-METHepatocyte growth factor receptor precursor factor receptor) MGMTO-6-methylguanine-DNA MGMT Methylated-DNA--protein-cysteinemethyltransferase methyltransferase MKI67, KI67 antigen identified bymonoclonal Ki67, Ki-67 Antigen KI-67 antibody Ki-67 MLH1 mutL homolog 1,colon cancer, MLH1 DNA mismatch repair protein Mlh1 nonpolyposis type 2(E. coli) MMR mismatch repair (refers to MLH1, MSH2, MSH5) MSH2 mutShomolog 2, colon cancer, MSH2 DNA mismatch repair protein Msh2nonpolyposis type 1 (E. coli) MSH5 mutS homolog 5 (E. coli) MSH5, MutSprotein homolog 5 hMSH5 MYC, c- v-myc myelocytomatosis viral oncogeneMYC, c-MYC Myc proto-oncogene protein MYC homolog (avian) NBN, P95nibrin NBN, p95 Nibrin NDGR1 N-myc downstream regulated 1 NDGR1 ProteinNDGR1 NFKB1 nuclear factor of kappa light polypeptide NFKB1 Nuclearfactor NF-kappa-B p105 subunit gene enhancer in B-cells 1 NFKB2 nuclearfactor of kappa light polypeptide NFKB2 Nuclear factor NF-kappa-B p100subunit gene enhancer in B-cells 2 (p49/p100) NFKBIA nuclear factor ofkappa light polypeptide NFKBIA NF-kappa-B inhibitor alpha gene enhancerin B-cells inhibitor, alpha NRAS neuroblastoma RAS viral (v-ras) NRASGTPase NRas, Transforming protein N-Ras oncogene homolog ODC1 ornithinedecarboxylase 1 ODC Ornithine decarboxylase OGFR opioid growth factorreceptor OGFR Opioid growth factor receptor PARP1 poly (ADP-ribose)polymerase 1 PARP-1 Poly [ADP-ribose] polymerase 1 PDGFC plateletderived growth factor C PDGF-C, Platelet-derived growth factor Cprecursor VEGF-E PDGFR platelet-derived growth factor receptor PDGFRPlatelet-derived growth factor receptor PDGFRA platelet-derived growthfactor receptor, PDGFRA, Alpha-type platelet-derived growth factor alphapolypeptide PDGFR2, receptor precursor CD140 A PDGFRB platelet-derivedgrowth factor receptor, PDGFRB, Beta-type platelet-derived growth factorbeta polypeptide PDGFR, receptor precursor PDGFR1, CD140 B PGRprogesterone receptor PR Progesterone receptor PIK3CAphosphoinositide-3-kinase, catalytic, PI3K subunitphosphoinositide-3-kinase, catalytic, alpha alpha polypeptide p110αpolypeptide POLA1 polymerase (DNA directed), alpha 1, POLA, DNApolymerase alpha catalytic subunit catalytic subunit; polymerase (DNAPOLA1, p180 directed), alpha, polymerase (DNA directed), alpha 1 PPARG,peroxisome proliferator-activated PPARG Peroxisomeproliferator-activated receptor PPARG1, receptor gamma gamma PPARG2,PPAR- gamma, NR1C3 PPARGC1A, peroxisome proliferator-activatedPGC-1-alpha, Peroxisome proliferator-activated receptor LEM6, receptorgamma, coactivator 1 alpha PPARGC-1- gamma coactivator 1-alpha;PPAR-gamma PGC1, alpha coactivator 1-alpha PGC1A, PPARGC1 PSMD9, P27proteasome (prosome, macropain) 26S p27 26S proteasome non-ATPaseregulatory subunit, non-ATPase, 9 subunit 9 PTEN, phosphatase and tensinhomolog PTEN Phosphatidylinositol-3,4,5-trisphosphate 3- MMAC1,phosphatase and dual-specificity protein TEP1 phosphatase; Mutated inmultiple advanced cancers 1 PTPN12 protein tyrosine phosphatase, non-PTPG1 Tyrosine-protein phosphatase non-receptor receptor type 12 type12; Protein-tyrosine phosphatase G1 RAF1 v-raf-1 murine leukemia viraloncogene RAF, RAF-1, RAF proto-oncogene serine/threonine- homolog 1c-RAF protein kinase RARA retinoic acid receptor, alpha RAR, RAR-Retinoic acid receptor alpha alpha, RARA ROS1, ROS, c-ros oncogene 1,receptor tyrosine ROS1, ROS Proto-oncogene tyrosine-protein kinase ROSMCF3 kinase RRM1 ribonucleotide reductase M1 RRM1, RR1Ribonucleoside-diphosphate reductase large subunit RRM2 ribonucleotidereductase M2 RRM2, Ribonucleoside-diphosphate reductase RR2M, RR2subunit M2 RRM2B ribonucleotide reductase M2 B (TP53 RRM2B,Ribonucleoside-diphosphate reductase inducible) P53R2 subunit M2 B RXRBretinoid X receptor, beta RXRB Retinoic acid receptor RXR-beta RXRGretinoid X receptor, gamma RXRG, Retinoic acid receptor RXR-gamma RXRCSIK2 salt-inducible kinase 2 SIK2, Salt-inducible protein kinase 2;Q9H0K1 Serine/threonine-protein kinase SIK2 SLC29A1 solute carrierfamily 29 (nucleoside ENT-1 Equilibrative nucleoside transporter 1transporters), member 1 SPARC secreted protein, acidic, cysteine-richSPARC SPARC precursor; Osteonectin (osteonectin) SRC v-src sarcoma(Schmidt-Ruppin A-2) SRC Proto-oncogene tyrosine-protein kinase Srcviral oncogene homolog (avian) SSTR1 somatostatin receptor 1 SSTR1,Somatostatin receptor type 1 SSR1, SS1R SSTR2 somatostatin receptor 2SSTR2, Somatostatin receptor type 2 SSR2, SS2R SSTR3 somatostatinreceptor 3 SSTR3, Somatostatin receptor type 3 SSR3, SS3R SSTR4somatostatin receptor 4 SSTR4, Somatostatin receptor type 4 SSR4, SS4RSSTR5 somatostatin receptor 5 SSTR5, Somatostatin receptor type 5 SSR5,SS5R TK1 thymidine kinase 1, soluble TK1, KITH Thymidine kinase,cytosolic TLE3 transducin-like enhancer of split 3 TLE3 Transducin-likeenhancer protein 3 (E(sp1) homolog, Drosophila) TNF tumor necrosisfactor (TNF superfamily, TNF, TNF- Tumor necrosis factor precursormember 2) alpha, TNF-a TOP1, topoisomerase (DNA) I TOP1, DNAtopoisomerase 1 TOPO1 TOPO1 TOP2A, topoisomerase (DNA) II alpha 170 kDaTOP2A, DNA topoisomerase 2-alpha; Topoisomerase TOPO2A TOP2, II alphaTOPO2A TOP2B, topoisomerase (DNA) II beta 180 kDa TOP2B, DNAtopoisomerase 2-beta; Topoisomerase TOPO2B TOPO2B II beta TP53 tumorprotein p53 p53 Cellular tumor antigen p53 TUBB3 tubulin, beta 3 BetaIII Tubulin beta-3 chain tubulin, TUBB3, TUBB4 TXN thioredoxin TXN, TRX,Thioredoxin TRX-1 TXNRD1 thioredoxin reductase 1 TXNRD1, Thioredoxinreductase 1, cytoplasmic; TXNR Oxidoreductase TYMS, TS thymidylatesynthetase TYMS, TS Thymidylate synthase VDR vitamin D(1,25-dihydroxyvitamin D3) VDR Vitamin D3 receptor receptor VEGFA,vascular endothelial growth factor A VEGF-A, Vascular endothelial growthfactor A VEGF VEGF precursor VEGFC vascular endothelial growth factor CVEGF-C Vascular endothelial growth factor C precursor VHL vonHippel-Lindau tumor suppressor VHL Von Hippel-Lindau disease tumorsuppressor YES1 v-yes-1 Yamaguchi sarcoma viral YES1, Yes,Proto-oncogene tyrosine-protein kinase Yes oncogene homolog 1 p61-YesZAP70 zeta-chain (TCR) associated protein ZAP-70 Tyrosine-protein kinaseZAP-70 kinase 70 kDa

The biomarkers used for biosignature discovery can comprise includemarkers commonly associated with vesicles, including without limitationone or more of vesicle biomarker in Table 11. Other biomarkers can beselected from those disclosed in the ExoCarta database, available atexocarta.ludwig.edu.au, which discloses proteins and RNA moleculesidentified in exosomes. See also Mathivanan and Simpson, ExoCarta: Acompendium of exosomal proteins and RNA. Proteomics. 2009 Nov.9(21):4997-5000.

The biomarkers used for biosignature discovery can comprise includemarkers commonly associated with vesicles, including without limitationone or more of A33, a33 n15, AFP, ALA, ALIX, ALP, AnnexinV, APC, ASCA,ASPH (246-260), ASPH (666-680), ASPH (A-10), ASPH (D01P), ASPH (D03),ASPH (G-20), ASPH(H-300), AURKA, AURKB, B7H3, B7H4, BCA-225, BCNP1,BDNF, BRCA, CA125 (MUC16), CA-19-9, C-Bir, CD1.1, CD10, CD174 (Lewis y),CD24, CD44, CD46, CD59 (MEM-43), CD63, CD66e CEA, CD73, CD81, CD9, CDA,CDAC1 1a2, CEA, C-Erb2, C-erbB2, CRMP-2, CRP, CXCL12, CYFRA21-1, DLL4,DR3, EGFR, Epcam, EphA2, EphA2 (H-77), ER, ErbB4, EZH2, FASL, FRT, FRTc.f23, GDF15, GPCR, GPR30, Gro-alpha, HAP, HBD 1, HBD2, HER 3 (ErbB3),HSP, HSP70, hVEGFR2, iC3b, IL 6 Unc, IL-1B, 1L6 Unc, IL6R, IL8, IL-8,INSIG-2, KLK2, L1CAM, LAMN, LDH, MACC-1, MAPK4, MART-1, MCP-1, M-CSF,MFG-E8, MIC1, MIF, MIS RII, MMG, MMP26, MMP7, MMP9, MS4A1, MUC1, MUC1seq1, MUC1 seq11A, MUC17, MUC2, Ncam, NGAL, NPGP/NPFF2, OPG, OPN, p53,p53, PA2G4, PBP, PCSA, PDGFRB, PGP9.5, PIM1, PR (B), PRL, PSA, PSMA,PSME3, PTEN, R5-CD9 Tube 1, Reg IV, RUNX2, SCRN1, seprase, SERPINB3,SPARC, SPB, SPDEF, SRVN, STAT 3, STEAP1, TF (FL-295), TFF3, TGM2,TIMP-1, TIMP1, TIMP2, TMEM211, TMPRSS2, TNF-alpha, Trail-R2, Trail-R4,TrKB, TROP2, Tsg 101, TWEAK, UNC93A, VEGF A, and YPSMA-1. The biomarkerscan include one or more of NSE, TRIM29, CD63, CD151, ASPH, LAMP2,TSPAN1, SNAIL, CD45, CKS1, NSE, FSHR, OPN, FTH1, PGP9, ANNEXIN 1, SPD,CD81, EPCAM, PTH1R, CEA, CYTO 7, CCL2, SPA, KRAS, TWIST1, AURKB, MMP9,P27, MMP1, HLA, HIF, CEACAM, CENPH, BTUB, INTG b4, EGFR, NACC1, CYTO 18,NAP2, CYTO 19, ANNEXIN V, TGM2, ERB2, BRCA1, B7H3, SFTPC, PNT, NCAM,MS4A1, P53, INGA3, MUC2, SPA, OPN, CD63, CD9, MUC1, UNCR3, PAN ADH, HCG,TIMP, PSMA, GPCR, RACK1, PCSA, VEGF, BMP2, CD81, CRP, PRO GRP, B7H3,MUC1, M2PK, CD9, PCSA, and PSMA. The biomarkers can also include one ormore of TFF3, MS4A1, EphA2, GAL3, EGFR, N-gal, PCSA, CD63, MUC1, TGM2,CD81, DR3, MACC-1, TrKB, CD24, TIMP-1, A33, CD66 CEA, PRL, MMP9, MMP7,TMEM211, SCRN1, TROP2, TWEAK, CDACC1, UNC93A, APC, C-Erb, CD10, BDNF,FRT, GPR30, P53, SPR, OPN, MUC2, GRO-1, tsg 101 and GDF 15. Inembodiments, the biomarkers used to discover a biosignature comprise oneor more of those shown in FIGS. 99, 100, 108A-C, 114A, and/or 115A-E ofInternational Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein.

One of skill will appreciate that any marker disclosed herein or thatcan be compared between two samples or sample groups of interest can beused to discover a novel biosignature for any given biological settingthat can be compared.

The one or more differences can then be used to form a candidatebiosignature for the particular phenotype, such as the diagnosis of acondition, diagnosis of a stage of a disease or condition, prognosis ofa condition, or theranosis of a condition. The novel biosignature canthen be used to identify the phenotype in other subjects. Thebiosignature of a vesicle for a new subject can be determined andcompared to the novel signature to determine if the subject has theparticular phenotype for which the novel biosignature was identifiedfrom.

For example, the biosignature of a subject with cancer can be comparedto another subject without cancer. Any differences can be used to form anovel biosignature for the diagnosis of the cancer. In anotherembodiment, the biosignature of a subject with an advanced stage ofcancer can be compared to another subject with a less advanced stage ofcancer. Any differences can be used to form a novel biosignature for theclassification of the stage of cancer. In yet another embodiment, thebiosignature of a subject with an advanced stage of cancer can becompared to another subject with a less advanced stage of cancer. Anydifferences can be used to form a novel biosignature for theclassification of the stage of cancer.

In one embodiment, the phenotype is drug resistance ornon-responsiveness to a therapeutic. One or more vesicles can beisolated from a non-responder to a particular treatment and thebiosignature of the vesicle determined. The biosignature of the vesicleobtained from the non-responsder can be compared to the biosignature ofa vesicle obtained from a responsder. Differences between thebiosignature from the non-responder can be compared to the biosignaturefrom the responder. The one or more differences can be a difference inany characteristic of the vesicle. For example, the level or amount ofvesicles in the sample, the half-life of the vesicle, the circulatinghalf-life of the vesicle, the metabolic half-life of the vesicle, theactivity of the vesicle, or any combination thereof, can differ betweenthe biosignature from the non-responder and the biosignature from theresponder.

In some embodiments, one or more biomarkers differ between thebiosignature from the non-responder and the biosignature from theresponder. For example, the expression level, presence, absence,mutation, variant, copy number variation, truncation, duplication,modification, molecular association of one or more biomarkers, or anycombination thereof, may differ between the biosignature from thenon-responder and the biosignature from the responder.

In some embodiments, the difference can be in the amount of drug or drugmetabolite present in the vesicle. Both the responder and non-respondercan be treated with a therapeutic. A comparison between the biosignaturefrom the responder and the biosignature from the non-responder can beperformed, the amount of drug or drug metabolite present in the vesiclefrom the responder differs from the amount of drug or drug metabolitepresent in the non-responder. The difference can also be in thehalf-life of the drug or drug metabolite. A difference in the amount orhalf-life of the drug or drug metabolite can be used to form a novelbiosignature for identifying non-responders and responders.

A vesicle useful for methods and compositions described herein can bediscovered by taking advantage of its physicochemical characteristics.For example, a vesicle can be discovered by its size, e.g., by filteringbiological matter in a known range from 30-120 nm in diameter.Size-based discovery methods, such as differential centrifugation,sucrose gradient centrifugation, or filtration have been used forisolation of a vesicle.

A vesicle can be discovered by its molecular components. Molecularproperty-based discovery methods include, but are not limited to,immunological isolation using antibodies recognizing moleculesassociated with vesicle. For example, a surface molecule associated witha vesicle includes, but not limited to, a MHC-II molecule, CD63, CD81,LAMP-1, Rab7 or Rab5.

Various techniques known in the art are applicable for validation andcharacterization of a vesicle. Techniques useful for validation andcharacterization of a vesicle includes, but is not limited to, westernblot, electron microscopy, immunohistochemistry, immunoelectronmicroscopy, FACS (Fluorescent activated cell sorting), electrophoresis(1 dimension, 2 dimension), liquid chromatography, mass spectrometry,MALDI-TOF (matrix assisted laser desorption/ionization-time of flight),ELISA, LC-MS-MS, and nESI (nanoelectrospray ionization). For exampleU.S. Pat. No. 2009/0148460 describes use of an ELISA method tocharacterize a vesicle. U.S. Pat. No. 2009/0258379 describes isolationof membrane vesicles from biological fluids.

Vesicles can be further analyzed for one or more nucleic acids, lipids,proteins or polypeptides, such as surface proteins or peptides, orproteins or peptides within a vesicle. Candidate peptides can beidentified by various techniques including mass spectrometry coupledwith purification methods such as liquid chromatography. A peptide canthen be isolated and its sequence can be identified by sequencing. Acomputer program that predicts a sequence based on exact mass of apeptide can also be used to reveal the sequence of a peptide isolatedfrom a vesicle. For example, LTQ-Orbitrap mass spectrometry can be usedfor high sensitivity and high accuracy peptide sequencing. LTQ-Orbitrapmethod has been described (Simpson et al, Expert Rev. Proteomics6:267-283, 2009), which is incorporated herein by reference in itsentirety.

Vesicle Compositions

Also provided herein is an isolated vesicle with a particularbiosignature. The isolated vesicle can comprise one or more biomarkersor biosignatures specific for specific cell type, or for characterizinga phenotype, such as described above. An isolated vesicle can alsocomprise one or more biomarkers, wherein the expression level of the oneor more biomarkers is higher, lower, or the same for an isolated vesicleas compared to an isolated vesicle derived from a normal cell (ie. acell derived from a subject without a phenotype of interest). Forexample, an isolated vesicle can comprise one or more biomarkersselected from the group consisting of: B7H3, PSCA, MFG-E8, Rab, STEAP,PSMA, PCSA, 5T4, miR-9, miR-629, miR-141, miR-671-3p, miR-491, miR-182,miR-125a-3p, miR-324-5p, miR-148b, and miR-222, wherein the expressionlevel of the one or more biomarkers is higher for an isolated vesicle ascompared those derived from a normal cell. The isolated vesicle cancomprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17,18, or 19 of the biomarkers selected from the group. The isolatedvesicle can further comprising one or more biomarkers selected from thegroup consisting of: EpCam, B7H3, PSMA, PSCA, PCSA, CD63, CD59, CD81, orCD9.

A composition comprising an isolated vesicle is also provided herein.The composition can comprise one or more isolated vesicles. For example,the composition can comprise a plurality of vesicles, or one or morepopulations of vesicles. The composition can be substantially enrichedfor vesicles. For example, the composition can be substantially absentof cellular debris, cells, or non-exosomal proteins, peptides, ornucleic acids (such as biological molecules not contained within thevesicles). The cellular debris, cells, or non-exosomal proteins,peptides, or nucleic acids, can be present in a biological sample alongwith vesicles. A composition can be substantially absent of cellulardebris, cells, or non-exosomal proteins, peptides, or nucleic acids(such as biological molecules not contained within the vesicles), can beobtained by any method disclosed herein, such as through the use of oneor more binding agents or capture agents for one or more vesicles. Thevesicles can comprise at least 30, 40, 50, 60, 70, 80, 90, 95 or 99% ofthe total composition, by weight or by mass. The vesicles of thecomposition can be a heterogeneous or homogeneous population ofvesicles. For example, a homogeneous population of vesicles comprisesvesicles that are homogeneous as to one or more properties orcharacteristics. For example, the one or more characteristics can beselected from a group consisting of: one or more of the same biomarkers,a substantially similar or identical biosignature, derived from the samecell type, vesicles of a particular size, and a combination thereof.

Thus, in some embodiments, the composition comprises a substantiallyenriched population of vesicles. The composition can be enriched for apopulation of vesicles that are at least 30, 40, 50, 60, 70, 80, 90, 95or 99% homogeneous as to one or more properties or characteristics. Forexample, the one or more characteristics can be selected from a groupconsisting of: one or more of the same biomarkers, a substantiallysimilar or identical biosignature, derived from the same cell type,vesicles of a particular size, and a combination thereof. For example,the population of vesicles can be homogeneous by all having a particularbiosignature, having the same biomarker, having the same biomarkercombination, or derived from the same cell type. In some embodiments,the composition comprises a substantially homogeneous population ofvesicles, such as a population with a specific biosignature, derivedfrom a specific cell, or both.

The population of vesicles can comprise one or more of the samebiomarkers. The biomarker can be any component such as any nucleic acid(e.g. RNA or DNA), protein, peptide, polypeptide, antigen, lipid,carbohydrate, or proteoglycan. For example, each vesicle in a populationcan comprise the same or identical one or more biomarkers. In someembodiments, each vesicle comprises the same 1, 2, 3, 4, 5, 6, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50, 75 or100 biomarkers.

The vesicle population comprising the same or identical biomarker caninclude each vesicle in the population having the same presence orabsence, expression level, mutational state, or modification of thebiomarker. For example, an enriched population of vesicle can comprisevesicles wherein each vesicle has the same biomarker present, the samebiomarker absent, the same expression level of a biomarker, the samemodification of a biomarker, or the same mutation of a biomarker. Thesame expression level of a biomarker can refer to a quantitative orqualitative measurement, such as the vesicles in the populationunderexpress, overexpress, or have the same expression level of abiomarker as compared to a reference level.

Alternatively, the same expression level of a biomarker can be anumerical value representing the expression of a biomarker that issimilar for each vesicle in a population. For example the copy number ofa miRNA, the amount of protein, or the level of mRNA of each vesicle,can be quantitatively similar for each vesicle in a population, suchthat the numerical amount of each vesicle is ±1, 2, 3, 4, 5, 6, 7, 8, 9,10, 15, or 20% from the amount in each other vesicle in the population,as such variations are appropriate.

In some embodiments, the composition comprises a substantially enrichedpopulation of vesicles, wherein the vesicles in the enriched populationhas a substantially similar or identical biosignature. The biosignaturecan comprise one or more characteristic of the vesicle, such as thelevel or amount of vesicles, temporal evaluation of the variation invesicle half-life, circulating vesicle half-life, metabolic half-life ofa vesicle, or the activity of a vesicle. The biosignature can alsocomprise the presence or absence, expression level, mutational state, ormodification of a biomarker, such as those described herein.

The biosignature of each vesicle in the population can be at least 30,40, 50, 60, 70, 80, 90, 95, or 99% identical. In some embodiments, thebiosignature of each vesicle is 100% identical. The biosignature of eachvesicle in the enriched population can have the same 1, 2, 3, 4, 5, 6,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 50,75 or 100 characteristics. For example, a biosignature of a vesicle inan enriched population can be the presence of a first biomarker, thepresence of a second biomarker, and the underexpression of a thirdbiomarker. Another vesicle in the same population can be 100% identical,having the same first and second biomarkers present and underexpressionof the third biomarker. Alternatively, a vesicle in the same populationcan have the same first and second biomarkers, but not haveunderexpression of the third biomarker.

In some embodiments, the composition comprises a substantially enrichedpopulation of vesicles, wherein the vesicles are derived from the samecell type. For example, the vesicles can all be derived from cells of aspecific tissue, cells from a specific tumor of interest or a diseasedtissue of interest, circulating tumor cells, or cells of maternal orfetal origin. The vesicles can all be derived from tumor cells. Thevesicles can all be derived from the same tissue or cells, includingwithout limitation lung, pancreas, stomach, intestine, bladder, kidney,ovary, testis, skin, colorectal, breast, prostate, brain, esophagus,liver, placenta, or fetal cells.

The composition comprising a substantially enriched population ofvesicles can also comprise vesicles are of a particular size. Forexample, the vesicles can all a diameter of greater than about 10, 20,or 30 nm. They can all have a diameter of about 10-1000 nm, e.g., about30-800 nm, about 30-200 nm, or about 30-100 nm. In some embodiments, thevesicles can all have a diameter of less than 10,000 nm, 1000 nm, 800nm, 500 nm, 200 nm, 100 nm or 50 nm.

The population of vesicles homogeneous for one or more characteristicscan comprises at least about 30, 40, 50, 60, 70, 80, 90, 95, or 99% ofthe total vesicle population of the composition. In some embodiments, acomposition comprising a substantially enriched population of vesiclescomprises at least 2, 3, 4, 5, 10, 20, 25, 50, 100, 250, 500, or 1000times the concentration of vesicle as compared to a concentration of thevesicle in a biological sample from which the composition was derived.In yet other embodiments, the composition can further comprise a secondenriched population of vesicles, wherein the population of vesicles isat least 30% homogeneous as to one or more characteristics, as describedherein.

Multiplex analysis can be used to obtain a composition substantiallyenriched for more than one population of vesicles, such as at least 2,3, 4, 5, 6, 7, 8, 9, 10 vesicle, populations. Each substantiallyenriched vesicle population can comprise at least 5, 10, 15, 20, 25, 30,35, 40, 45, 46, 47, 48, or 49% of the composition, by weight or by mass.In some embodiments, the substantially enriched vesicle populationcomprises at least about 30, 40, 50, 60, 70, 80, 90, 95, or 99% of thecomposition, by weight or by mass.

A substantially enriched population of vesicles can be obtained by usingone or more methods, processes, or systems as disclosed herein. Forexample, isolation of a population of vesicles from a sample can beperformed by using one or more binding agents for one or more biomarkersof a vesicle, such as using two or more binding agents that target twoor more biomarkers of a vesicle. One or more capture agents can be usedto obtain a substantially enriched population of vesicles. One or moredetection agents can be used to identify a substantially enrichedpopulation of vesicles.

In one embodiment, a population of vesicles with a particularbiosignature is obtained by using one or more binding agents for thebiomarkers of the biosignature. The vesicles can be isolated resultingin a composition comprising a substantially enriched population ofvesicles with the particular biosignature. In another embodiment, apopulation of vesicles with a particular biosignature of interest can beobtained by using one or more binding agents for biomarkers that are nota component of the biosignature of interest. Thus, the binding agentscan be used to remove the vesicles that do not have the biosignature ofinterest and the resulting composition is substantially enriched for thepopulation of vesicles with the particular biosignature of interest. Theresulting composition can be substantially absent of the vesiclescomprising a biomarker for the binding agent.

International Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein.

Detection System and Kits

Also provided is a detection system configured to determine one or morebiosignatures for a vesicle. The detection system can be used to detecta heterogeneous population of vesicles or one or more homogeneouspopulation of vesicles. The detection system can be configured to detecta plurality of vesicles, wherein at least a subset of the plurality ofvesicles comprises a different biosignature from another subset of theplurality of vesicles. The detection system detect at least 2, 3, 4, 5,6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, or 100 differentsubsets of vesicles, wherein each subset of vesicles comprises adifferent biosignature. For example, a detection system, such as usingone or more methods, processes, and compositions disclosed herein, canbe used to detect at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,40, 50, 60, 70, 80, 90, or 100 different populations of vesicles.

The detection system can be configured to assess at least 2, 3, 4, 5, 6,7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500,5000, 7500, 10,000, 100,000, 150,000, 200,000, 250,000, 300,000,350,000, 400,000, 450,000, 500,000, 750,000, or 1,000,000 differentbiomarkers for one or more vesicles. In some embodiments, the one ormore biomarkers are selected from any of Tables 3-5, or as disclosedherein. The detection system can be configured to assess a specificpopulation of vesicles, such as vesicles from a specific cell-of-origin,or to assess a plurality of specific populations of vesicles, whereineach population of vesicles has a specific biosignature.

The detection system can be a low density detection system or a highdensity detection system. For example, a low density detection systemcan detect up to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 different vesiclepopulations, whereas a high density detection system can detect at leastabout 15, 20, 25, 50, or 100 different vesicle populations In anotherembodiment, a low density detection system can detect up to about 100,200, 300, 400, or 500 different biomarkers, whereas a high densitydetection system can detect at least about 750, 1000, 2000, 3000, 4000,5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000, 25,000, 50,000,or 100,000 different biomarkers. In yet another embodiment, a lowdensity detection system can detect up to about 100, 200, 300, 400, or500 different biosignatures or biomarker combinations, whereas a highdensity detection system can detect at least about 750, 1000, 2000,3000, 4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000,25,000, 50,000, or 100,000 biosignatures or biomarker combinations.

The detection system can comprise a probe that selectively hybridizes toa vesicle. The detection system can comprise a plurality of probes todetect a vesicle. In some embodiments, a plurality of probes is used todetect the amount of vesicles in a heterogeneous population of vesicles.In yet other embodiments, a plurality of probes is used to detect ahomogeneous population of vesicles. A plurality of probes can be used toisolate or detect at least two different subsets of vesicles, whereineach subset of vesicles comprises a different biosignature.

A detection system, such as using one or more methods, processes, andcompositions disclosed herein, can comprise a plurality of probesconfigured to detect, or isolate, such as using one or more methods,processes, and compositions disclosed herein at least 2, 3, 4, 5, 6, 7,8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, or 100 differentsubsets of vesicles, wherein each subset of vesicles comprises adifferent biosignature.

For example, a detection system can comprise a plurality of probesconfigured to detect at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30, 40, 50, 60, 70, 80, 90, or 100 different populations of vesicles.The detection system can comprise a plurality of probes configured toselectively hybridize to at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500, 10,000,100,000, 150,000, 200,000, 250,000, 300,000, 350,000, 400,000, 450,000,500,000, 750,000, or 1,000,000 different biomarkers for one or morevesicles. In some embodiments, the one or more biomarkers are selectedfrom any of Tables 3-5, or as disclosed herein. The plurality of probescan be configured to assess a specific population of vesicles, such asvesicles from a specific cell-of-origin, or to assess a plurality ofspecific populations of vesicles, wherein each population of vesicleshas a specific biosignature.

The detection system can be a low density detection system or a highdensity detection system comprising probes to detect vesicles. Forexample, a low density detection system can comprise probes to detect upto 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 different vesicle populations,whereas a high density detection system can comprise probes to detect atleast about 15, 20, 25, 50, or 100 different vesicle populations. Inanother embodiment, a low density detection system can comprise probesto detect up to about 100, 200, 300, 400, or 500 different biomarkers,whereas a high density detection system can comprise probes to detect atleast about 750, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9,000,10,000, 15,000, 20,000, 25,000, 50,000, or 100,000 different biomarkers.In yet another embodiment, a low density detection system can compriseprobes to detect up to about 100, 200, 300, 400, or 500 differentbiosignatures or biomarker combinations, whereas a high densitydetection system can comprise probes to detect at least about 750, 1000,2000, 3000, 4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000,25,000, 50,000, or 100,000 biosignatures or biomarker combinations.

The probes can be specific for detecting a specific vesicle population,for example a vesicle with a particular biosignature, and as describedabove. A plurality of probes for detecting prostate specific vesicles isalso provided. A plurality of probes can comprise probes for detectingone or more of the biomarkers in Tables 3-5. The plurality of probes canalso comprise one or more probes for detecting one or more of thebiomarkers in Tables 3-5.

A plurality of probes for detecting one or more miRNAs of a vesicle cancomprise probes for detecting one or more of the following miRNAs:miR-9, miR-629, miR-141, miR-671-3p, miR-491, miR-182, miR-125a-3p,miR-324-5p, miR-148b, and miR-222. In another embodiment, the pluralityof probes comprises one or more probes for detecting EpCam, CD9, PCSA,CD63, CD81, PSMA, B7H3, PSCA, ICAM, STEAP, and EGFR. In someembodiments, the plurality of probes comprises one or more probes fordetecting EpCam, CD9, PCSA, CD63, CD81, PSMA, and B7H3. In otherembodiments, the plurality of probes comprises one or more probes fordetecting EpCam, CD9, PCSA, CD63, CD81, PSMA, B7H3, PSCA, ICAM, STEAP,and EGFR. In yet another embodiment, a subset of the plurality of probesare capture agents for one or more of EpCam, CD9, PCSA, CD63, CD81,PSMA, B7H3, PSCA, ICAM, STEAP, and EGFR, and another subset are probesfor detecting one or more of CD9, CD63, and CD81. A plurality of probescan also comprises one or more probes for detecting r miR-92a-2*,miR-147, miR-574-5p, or a combination thereof. A plurality of probes canalso comprise one or more probes for detecting miR-548c-5p, miR-362-3p,miR-422a, miR-597, miR-429, miR-200a, miR-200b or a combination thereof.A plurality of probes can also comprise one or more probes for detectingEpCam, CK, and CD45. In some embodiments, the one or more probes may becapture agents. In another embodiment, the probes may be detectionagents. In yet another embodiment, the plurality of probes comprisescapture and detection agents.

The probes, such as capture agents, may be attached to a solidsubstrate, such as an array or bead. Alternatively, the probes, such asdetection agents, are not attached. The detection system may be an arraybased system, a sequencing system, a PCR-based system, or a bead-basedsystem, such as described above. The detection system can also be amicrofluidic device as described above.

The detection system may be part of a kit. Alternatively, the kit maycomprise the one or more probe sets or plurality of probes, as describedherein. The kit may comprise probes for detecting a vesicle or aplurality of vesicles, such as vesicles in a heterogeneous population.The kit may comprise probes for detecting a homogeneous population ofvesicles. For example, the kit may comprise probes for detecting apopulation of specific cell-of-origin vesicles, or vesicles with thesame specific biosignature

Computer Systems

A vesicle can be assayed for molecular features, for example, bydetermining an amount, presence or absence of one or more biomarkers.The data generated can be used to produce a biosignature, which can bestored and analyzed by a computer system, such as shown in FIG. 3. Theassaying or correlating of the biosignature with one or more phenotypescan also be performed by computer systems, such as by using computerexecutable logic.

A computer system, such as shown in FIG. 3, can be used to transmit dataand results following analysis. Accordingly, FIG. 3 is a block diagramshowing a representative example logic device through which results froma vesicle can be analyzed and the analysis reported or generated. FIG. 3shows a computer system (or digital device) 800 to receive and storedata generated from a vesicle, analyze of the data to generate one ormore biosignatures, and produce a report of the one or morebiosignatures or phenotype characterization. The computer system canalso perform comparisons and analyses of biosignatures generated, andtransmit the results. Alternatively, the computer system can receive rawdata of vesicle analysis, such as through transmission of the data overa network, and perform the analysis.

The computer system 800 may be understood as a logical apparatus thatcan read instructions from media 811 and/or network port 805, which canoptionally be connected to server 809 having fixed media 812. The systemshown in FIG. 3 includes CPU 801, disk drives 803, optional inputdevices such as keyboard 815 and/or mouse 816 and optional monitor 807.Data communication can be achieved through the indicated communicationmedium to a server 809 at a local or a remote location. Thecommunication medium can include any means of transmitting and/orreceiving data. For example, the communication medium can be a networkconnection, a wireless connection or an internet connection. Such aconnection can provide for communication over the World Wide Web. It isenvisioned that data relating to the present invention can betransmitted over such networks or connections for reception and/orreview by a party 822. The receiving party 822 can be but is not limitedto an individual, a health care provider or a health care manager. Thus,the information and data on a test result can be produced anywhere inthe world and transmitted to a different location. For example, when anassay is conducted in a differing building, city, state, country,continent or offshore, the information and data on a test result may begenerated and cast in a transmittable form as described above. The testresult in a transmittable form thus can be imported into the U.S. toreceiving party 822. Accordingly, the present invention also encompassesa method for producing a transmittable form of information on thediagnosis of one or more samples from an individual. The methodcomprises the steps of (1) determining a diagnosis, prognosis,theranosis or the like from the samples according to methods of theinvention; and (2) embodying the result of the determining step into atransmittable form. The transmittable form is the product of theproduction method. In one embodiment, a computer-readable mediumincludes a medium suitable for transmission of a result of an analysisof a biological sample, such as biosignatures. The medium can include aresult regarding a vesicle, such as a biosignature of a subject, whereinsuch a result is derived using the methods described herein.

EXAMPLES Example 1 Purification of Vesicles from Prostate Cancer CellLines

Prostate cancer cell lines are cultured for 3-4 days in culture mediacontaining 20% FBS (fetal bovine serum) and 1% P/S/G. The cells are thenpre-spun for 10 minutes at 400×g at 4° C. The supernatant is kept andcentrifuged for 20 minutes at 2000×g at 4. The supernatant containingvesicles can be concentrated using a Millipore Centricon Plus-70 (Cat#UFC710008 Fisher).

The Centricon is pre washed with 30 mls of PBS at 1000×g for 3 minutesat room temperature. Next, 15-70 mls of the pre-spun cell culturesupernatant is poured into the Concentrate Cup and is centrifuged in aSwing Bucket Adapter (Fisher Cat #75-008-144) for 30 minutes at 1000×gat room temperature.

The flow through in the Collection Cup is poured off. The volume in theConcentrate Cup is brought back up to 60 mls with any additionalsupernatant. The Concentrate Cup is centrifuged for 30 minutes at 1000×gat room temperature to concentrate the cell supernatant.

The Concentrate Cup is washed by adding 70 mls of PBS and centrifugedfor 30-60 minutes at 1000×g until approximately 2 mls remains. Thevesicles are removed from the filter by inverting the concentrate intothe small sample cup and centrifuge for 1 minute at 4° C. The volume isbrought up to 25 mls with PBS. The vesicles are now concentrated and areadded to a 30% Sucrose Cushion.

To make a cushion, 4 mls of Tris/30% Sucrose/D2O solution (30 gprotease-free sucrose, 2.4 g Tris base, 50 ml D2O, adjust pH to 7.4 with10N NCL drops, adjust volume to 100 mls with D2O, sterilize by passingthru a 0.22-um filter) is loaded to the bottom of a 30 ml V bottom thinwalled Ultracentrifuge tube. The diluted 25 mls of concentrated vesiclesis gently added above the sucrose cushion without disturbing theinterface and is centrifuged for 75 minutes at 100,000×g at 4° C. The˜25 mls above the sucrose cushion is carefully removed with a 10 mlpipet and the ˜3.5 mls of vesicles is collected with a fine tip transferpipet (SAMCO 233) and transferred to a fresh ultracentrifuge tube, where30 mls PBS is added. The tube is centrifuged for 70 minutes at 100,000×gat 4° C. The supernatant is poured off carefully. The pellet isresuspended in 200 ul PBS and can be stored at 4° C. or used for assays.A BCA assay (1:2) can be used to determine protein content and Westernblotting or electron micrography can be used to determine vesiclepurification.

Example 2 Purification of Vesicles from VCaP and 22Rv1

Vesicles from Vertebral-Cancer of the Prostate (VCaP) and 22Rv1, a humanprostate carcinoma cell line, derived from a human prostatic carcinomaxenograft (CWR22R) were collected by ultracentrifugation by firstdiluting plasma with an equal volume of PBS (1 ml). The diluted fluidwas transferred to a 15 ml falcon tube and centrifuged 30 minutes at2000×g 4° C. The supernatant (˜2 mls) was transferred to anultracentrifuge tube 5.0 ml PA thinwall tube (Sorvall #03127) andcentrifuged at 12,000×g, 4° C. for 45 minutes.

The supernatant (˜2 mls) was transferred to a new 5.0 ml ultracentrifugetubes and filled to maximum volume with addition of 2.5 mls PBS andcentrifuged for 90 minutes at 110,000×g, 4° C. The supernatant waspoured off without disturbing the pellet and the pellet resuspended with1 ml PBS. The tube was filled to maximum volume with addition of 4.5 mlof PBS and centrifuged at 110,000×g, 4° C. for 70 minutes.

The supernatant was poured off without disturbing the pellet and anadditional 1 ml of PBS was added to wash the pellet. The volume wasincreased to maximum volume with the addition of 4.5 mls of PBS andcentrifuged at 110,000×g for 70 minutes at 4° C. The supernatant wasremoved with P-1000 pipette until ˜100 μl of PBS was in the bottom ofthe tube. The ˜90 μl remaining was removed with P-200 pipette and thepellet collected with the ˜10 μl of PBS remaining by gently pipettingusing a P-20 pipette into the microcentrifuge tube. The residual pelletwas washed from the bottom of a dry tube with an additional 5 μl offresh PBS and collected into microcentrifuge tube and suspended inphosphate buffered saline (PBS) to a concentration of 500 μg/ml.

Example 3 Plasma Collection and Vesicle Purification

Blood is collected via standard venipuncture in a 7 ml K2-EDTA tube. Thesample is spun at 400 g for 10 minutes in a 4° C. centrifuge to separateplasma from blood cells (SORVALL Legend RT+ centrifuge). The supernatant(plasma) is transferred by careful pipetting to 15 ml Falcon centrifugetubes. The plasma is spun at 2,000 g for 20 minutes and the supernatantis collected.

For storage, approximately 1 ml of the plasma (supernatant) is aliquotedto a cryovials, placed in dry ice to freeze them and stored in −80° C.Before vesicle purification, if samples were stored at −80° C., samplesare thawed in a cold water bath for 5 minutes. The samples are mixed endover end by hand to dissipate insoluble material.

In a first prespin, the plasma is diluted with an equal volume of PBS(example, approximately 2 ml of plasma is diluted with 2 ml of PBS). Thediluted fluid is transferred to a 15 ml Falcon tube and centrifuged for30 minutes at 2000×g at 4° C.

For a second prespin, the supernatant (approximately 4 mls) is carefullytransferred to a 50 ml Falcon tube and centrifuged at 12,000×g at 4° C.for 45 minutes in a Sorval.

In the isolation step, the supernatant (approximately 2 mls) iscarefully transferred to a 5.0 ml ultracentrifuge PA thinwall tube(Sorvall #03127) using a P1000 pipette and filled to maximum volume withan additional 0.5 mls of PBS. The tube is centrifuged for 90 minutes at110,000×g at 4° C.

In the first wash, the supernatant is poured off without disturbing thepellet. The pellet is resuspended or washed with 1 ml PBS and the tubeis filled to maximum volume with an additional 4.5 ml of PBS. The tubeis centrifuged at 110,000×g at 4° C. for 70 minutes. A second wash isperformed by repeating the same steps.

The vesicles are collected by removing the supernatant with P-1000pipette until approximately 100 μl of PBS is in the bottom of the tube.Approximately 90 μl of the PBS is removed and discarded with P-200pipette. The pellet and remaining PBS is collected by gentle pipettingusing a P-20 pipette. The residual pellet is washed from the bottom ofthe dry tube with an additional 5 μl of fresh PBS and collected into amicrocentrifuge tube.

Example 4 Analysis of Vesicles Using Antibody-Coupled Microspheres andDirectly Conjugated Antibodies

This example demonstrates the use of particles coupled to an antibody,where the antibody captures the vesicles. See, e.g., FIG. 2A. Anantibody, the detector antibody, is directly coupled to a label, and isused to detect a biomarker on the captured vesicle.

First, an antibody-coupled microsphere set is selected (Luminex, Austin,Tex.). The microsphere set can comprise various antibodies, and thusallows multiplexing. The microspheres are resuspended by vortex andsonication for approximately 20 seconds. A Working Microsphere Mixtureis prepared by diluting the coupled microsphere stocks to a finalconcentration of 100 microspheres of each set/μL in Startblock (Pierce(37538)). 50 μL of Working Microsphere Mixture is used for each well.Either PBS-1% BSA or PBS-BN (PBS, 1% BSA, 0.05% Azide, pH 7.4) may beused as Assay Buffer.

A 1.2 μm Millipore filter plate is pre-wet with 100 μl/well of PBS-1%BSA (Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and aspirated by vacuummanifold. An aliquot of 50 μl of the Working Microsphere Mixture isdispensed into the appropriate wells of the filter plate (MilliporeMultiscreen HTS (MSBVN1250)). A 50 μl aliquot of standard or sample isdispensed into to the appropriate wells. The filter plate is covered andincubated for 60 minutes at room temperature on a plate shaker. Theplate is covered with a sealer, placed on the orbital shaker and set to900 for 15-30 seconds to re-suspend the beads. Following that the speedis set to 550 for the duration of the incubation.

The supernatant is aspirated by vacuum manifold (less than 5 inches Hgin all aspiration steps). Each well is washed twice with 100 μl ofPBS-1% BSA (Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and is aspiratedby vacuum manifold. The microspheres are resuspended in 50 μL of PBS-1%BSA (Sigma (P3688-10PAK+0.05% NaAzide (S8032))). The PE conjugateddetection antibody is diluted to 4 μg/mL (or appropriate concentration)in PBS-1% BSA (Sigma (P3688-10PAK+0.05% NaAzide (S8032))). (Note: 50 μLof diluted detection antibody is required for each reaction.) A 50 μlaliquot of the diluted detection antibody is added to each well. Thefilter plate is covered and incubated for 60 minutes at room temperatureon a plate shaker. The filter plate is covered with a sealer, placed onthe orbital shaker and set to 900 for 15-30 seconds to re-suspend thebeads. Following that the speed is set to 550 for the duration of theincubation. The supernatant is aspirated by vacuum manifold. The wellsare washed twice with 100 μl of PBS-1% BSA (Sigma (P3688-10PAK+0.05%NaAzide (S8032))) and aspirated by vacuum manifold. The microspheres areresuspended in 100 μl of PBS-1% BSA (Sigma (P3688-10PAK+0.05% NaAzide(S8032))). The microspheres are analyzed on a Luminex analyzer accordingto the system manual.

Example 5 Analysis of Vesicles Using Antibody-Coupled Microspheres andBiotinylated Antibody

This example demonstrates the use of particles coupled to an antibody,where the antibody captures the vesicles. An antibody, the detectorantibody, is biotinylated. A label coupled to streptavidin is used todetect the biomarker.

First, the appropriate antibody-coupled microsphere set is selected(Luminex, Austin, Tex.). The microspheres are resuspended by vortex andsonication for approximately 20 seconds. A Working Microsphere Mixtureis prepared by diluting the coupled microsphere stocks to a finalconcentration of 50 microspheres of each set/μL in Startblock (Pierce(37538)). (Note: 50 μl of Working Microsphere Mixture is required foreach well.) Beads in Start Block should be blocked for 30 minutes and nomore than 1 hour.

A 1.2 μm Millipore filter plate is pre-wet with 100 μl/well of PBS-1%BSA+Azide (PBS-BN) ((Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and isaspirated by vacuum manifold. A 50 μl aliquot of the Working MicrosphereMixture is dispensed into the appropriate wells of the filter plate(Millipore Multiscreen HTS (MSBVN1250)). A 50 μl aliquot of standard orsample is dispensed to the appropriate wells. The filter plate iscovered with a seal and is incubated for 60 minutes at room temperatureon a plate shaker. The covered filter plate is placed on the orbitalshaker and set to 900 for 15-30 seconds to re-suspend the beads.Following that, the speed is set to 550 for the duration of theincubation.

The supernatant is aspirated by a vacuum manifold (less than 5 inches Hgin all aspiration steps). Aspiration can be done with the Pall vacuummanifold. The valve is place in the full off position when the plate isplaced on the manifold. To aspirate slowly, the valve is opened to drawthe fluid from the wells, which takes approximately 3 seconds for the100 μl of sample and beads to be fully aspirated from the well. Once thesample drains, the purge button on the manifold is pressed to releaseresidual vacuum pressure from the plate.

Each well is washed twice with 100 μl of PBS-1% BSA+Azide (PBS-BN)(Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and is aspirates by vacuummanifold. The microspheres are resuspended in 50 μl of PBS-1% BSA+Azide(PBS-BN)((Sigma (P3688-10PAK+0.05% NaAzide (S8032)))

The biotinylated detection antibody is diluted to 4 μg/mL in PBS-1%BSA+Azide (PBS-BN) ((Sigma (P3688-10PAK+0.05% NaAzide (S8032))). (Note:50 μl of diluted detection antibody is required for each reaction.) A 50μl aliquot of the diluted detection antibody is added to each well.

The filter plate is covered with a sealer and is incubated for 60minutes at room temperature on a plate shaker. The plate is placed onthe orbital shaker and set to 900 for 15-30 seconds to re-suspend thebeads. Following that, the speed is set to 550 for the duration of theincubation.

The supernatant is aspirated by vacuum manifold. Aspiration can be donewith the Pall vacuum manifold. The valve is place in the full offposition when the plate is placed on the manifold. To aspirate slowly,the valve is opened to draw the fluid from the wells, which takesapproximately 3 seconds for the 100 ul of sample and beads to be fullyaspirated from the well. Once all of the sample is drained, the purgebutton on the manifold is pressed to release residual vacuum pressurefrom the plate.

Each well is washed twice with 100 μl of PBS-1% BSA+Azide (PBS-BN)((Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and is aspirated by vacuummanifold. The microspheres are resuspended in 50 μl of PBS-1% BSA (Sigma(P3688-10PAK+0.05% NaAzide (S8032))).

The streptavidin-R-phycoerythrin reporter (Molecular Probes 1 mg/ml) isdiluted to 4 μg/mL in PBS-1% BSA+Azide (PBS-BN). 50 μl of dilutedstreptavidin-R-phycoerythrin was used for each reaction. A 50 μl aliquotof the diluted streptavidin-R-phycoerythrin is added to each well.

The filter plate is covered with a sealer and is incubated for 60minutes at room temperature on a plate shaker. The plate is placed onthe orbital shaker and set to 900 for 15-30 seconds to re-suspend thebeads. Following that, the speed is set to 550 for the duration of theincubation.

The supernatant is aspirated by vacuum manifold. Aspiration can be donewith the Pall vacuum manifold. The valve is place in the full offposition when the plate is placed on the manifold. To aspirate slowly,the valve is opened to draw the fluid from the wells, which takesapproximately 3 seconds for the 100 ul of sample and beads to be fullyaspirated from the well. Once all of the sample is drained, the purgebutton on the manifold is pressed to release residual vacuum pressurefrom the plate.

Each well is washed twice with 100 μl of PBS-1% BSA+Azide (PBS-BN)((Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and is aspirated by vacuummanifold. The microspheres are resuspended in 100 μl of PBS-1% BSA+Azide(PBS-BN) ((Sigma (P3688-10PAK+0.05% NaAzide (S8032))) and analyzed onthe Luminex analyzer according to the system manual.

Example 6 Vesicle Concentration from Plasma

Supplies and Equipment:

Pall life sciences Acrodisc, 25 mm syringe filter w/1.2 μm, Versapormembrane (sterile) Part number: 4190; Pierce concentrators 7 ml/150 KMWCO (molecular weight cut off), Part number: 89922; BD syringe filter,10 ml, Part number: 305482; Sorvall Legend RT Plus Series BenchtopCentrifuge w 15 ml swinging bucket rotor; PBS, pH 7.4, Sigmacat#P3813-10PAK prepared in Sterile Molecular grade water; Co-polymer1.7 ml microfuge tubes, USA Scientific, cat#1415-2500. Water used forreagents is Sterile Filtered Molecular grade water (Sigma, cat#W4502).Handling of patient plasma is done in a biosafety hood.

Procedure:

1. Filter Procedure for Plasma Samples

-   -   1.1. Remove plasma samples from −80° C. (−65° C. to −85° C.)        freezer    -   1.2. Thaw samples in room temperature water (10-15 minutes).    -   1.3. Prepare syringe and filter by removing the number necessary        from their casing.    -   1.4. Pull plunger to draw 4 mL of sterile molecular grade water        into the syringe. Attach a 1.2 μm filter to the syringe tip and        pass contents through the filter onto the 7 ml/150 K MWCO Pierce        column.    -   1.5. Cap the columns and place in the swing bucket centrifuge at        spin at 1000×g in Sorvall Legend RT plus centrifuge for 4        minutes at 20° C. (16° C.-24° C.).    -   1.6. While spinning, disassemble the filter from syringe. Then        remove plunger from syringe.    -   1.7. Discard flow through from the tube and gently tap column on        paper towels to remove any residual water.    -   1.8. Measure and record starting volumes for all plasma samples.        Samples with a volume less than 900 μl may not be processed.    -   1.9. Place open syringe and filter on open Pierce column. Fill        open end of syringe with 5.2 mL of 1×PBS and pipette mix plasma        into PBS three to four times.    -   1.10. Replace the plunger of the syringe and slowly depress the        plunger until the contents of the syringe have passed through        the filter onto the Pierce column. Contents should pass through        the filter drop wise.

2. Microvesicle Concentration Centrifugation Protocol

-   -   2.1. Spin 7 ml/150 K MWCO Pierce columns at 2000×g at 20° C.        (16° C.-24° C.) for 60 minutes or until volume is reduced to        250-300 μL. If needed, spin for additional 15 minutes increments        to reach required volume.    -   2.2. At the conclusion of the spin, pipette mix on the column        15× (avoid creating bubbles) and withdraw volume (300 μL or        less) and transfer to a new 1.7 mL co-polymer tube.    -   2.3. The final volume of the plasma concentrate is dependent on        the initial volume of plasma. Plasma is concentrated to 300 ul        if the original plasma volume is 1 ml. If the original volume of        plasma is less than 1 ml, then the volume of concentrate should        be consistent with that ratio. For example, if the original        volume is 900 ul, then the volume of concentrate is 270 ul. The        equation to follow is: x=(y/1000)*300, where x is the final        volume of concentrate and y is the initial volume of plasma.    -   2.4. Record the sample volume and add 1×PBS to the sample to        make the final sample volume.    -   2.5. Store concentrated microvesicle sample at 4° C. (2° C. to        8° C.).

Calculations:

-   -   1. Final volume of concentrated plasma sample        -   x=(y/1000)*300, where x is the final volume of concentrate            and y is the initial volume of plasma.

Example 7 Capture of Vesicles Using Magnetic Beads

Vesicles isolated as described in Example 2 are used. Approximately 40μl of the vesicles are incubated with approximately 5 μg (˜50 μl) ofEpCam antibody coated Dynal beads (Invitrogen, Carlsbad, Calif.) and 50μl of Starting Block. The vesicles and beads are incubated with shakingfor 2 hours at 45° C. in a shaking incubator. The tube containing theDynal beads is placed on the magnetic separator for 1 minute and thesupernatant removed. The beads are washed twice and the supernatantremoved each time. Wash beads twice, discarding the supernatant eachtime.

Example 8 Detection of mRNA Transcripts in Vesicles

RNA from the bead-bound vesicles of Example 7 was isolated using theQiagen miRneasy™ kit, (Cat. No. 217061), according to the manufacturer'sinstructions.

The vesicles are homogenized in QIAzol™ Lysis Reagent (Qiagen Cat. No.79306). After addition of chloroform, the homogenate is separated intoaqueous and organic phases by centrifugation. RNA partitions to theupper, aqueous phase, while DNA partitions to the interphase andproteins to the lower, organic phase or the interphase. The upper,aqueous phase is extracted, and ethanol is added to provide appropriatebinding conditions for all RNA molecules from 18 nucleotides (nt)upwards. The sample is then applied to the RNeasy™ Mini spin column,where the total RNA binds to the membrane and phenol and othercontaminants are efficiently washed away. High quality RNA is theneluted in RNase-free water.

RNA from the VCAP bead captured vesicles was measured with the TaqmanTMPRSS:ERG fusion transcript assay (Kirsten D. Mertz et al. Neoplasia.2007 March; 9(3): 200-206.). RNA from the 22Rv1 bead captured vesicleswas measured with the Taqman SPINK1 transcript assay (Scott A. Tomlinset al. Cancer Cell 2008 Jun. 13(6):519-528). The GAPDH transcript(control transcript) was also measured for both sets of vesicle RNA.

Higher CT values indicate lower transcript expression. One change incycle threshold (CT) is equivalent to a 2 fold change, 3 CT differenceto a 4 fold change, and so forth, which can be calculated with thefollowing: 2̂^(CT1-CT2). This experiment shows a difference in CT of theexpression of the fusion transcript TMPRSS:ERG and the equivalentcaptured with the IgG2 negative control bead (FIG. 5). The samecomparison of the SPINK1 transcript in 22RV1 vesicles showed a CTdifference of 6.14 for a fold change of 70.5. Results with GAPDH weresimilar (not shown).

Example 9 Obtaining Serum Samples from Subjects

Blood is collected from subjects (both healthy subjects and subjectswith cancer) in EDTA tubes, citrate tubes or in a 10 ml Vacutainer SSTplus Blood Collection Tube (BD367985 or BD366643, BD Biosciences). Bloodis processed for plasma isolation within 2 h of collection.

Samples are allowed to sit at room temperature for a minimum of 30 minand a max of 2 h. Separation of the clot is accomplished bycentrifugation at 1,000-1,300×g at 4° C. for 15-20 min. The serum isremoved and dispensed in aliquots of 500 μl into 500 to 750 μlcryotubes. Specimens are stored at −80° C.

At a given sitting, the amount of blood drawn can range from ˜20 to ˜90ml. Blood from several EDTA tubes is pooled and transferred toRNase/DNase-free 50-ml conical tubes (Greiner), and centrifuged at1,200×g at room temperature in a Hettich Rotanta 460R benchtopcentrifuge for 10 min. Plasma is transferred to a fresh tube, leavingbehind a fixed height of 0.5 cm plasma supernatant above the pellet toavoid disturbing the pellet. Plasma is aliquoted, with inversion to mixbetween each aliquot, and stored at −80° C.

Example 10 RNA Isolation from Human Plasma and Serum Samples

Four hundred μl of human plasma or serum is thawed on ice and lysed withan equal volume of 2× Denaturing Solution (Ambion). RNA is isolatedusing the mirVana PARIS kit following the manufacturer's protocol forliquid samples (Ambion), modified such that samples are extracted twicewith an equal volume of acid-phenol chloroform (as supplied by theAmbion kit). RNA is eluted with 105 μl of Ambion elution solutionaccording to the manufacturer's protocol. The average volume of eluaterecovered from each column is about 80 μl.

A scaled-up version of the mirVana PARIS (Ambion) protocol is also used:10 ml of plasma is thawed on ice, two 5-ml aliquots are transferred to50-ml tubes, diluted with an equal volume of mirVana PARIS 2× DenaturingSolution, mixed thoroughly by vortexing for 30 s and incubated on icefor 5 min. An equal volume (10 ml) of acid/phenol/chloroform (Ambion) isthen added to each aliquot. The resulting solutions are vortexed for 1min and spun for 5 min at 8,000 rpm, 20° C. in a JA17 rotor. Theacid/phenol/chloroform extraction is repeated three times. The resultingaqueous volume is mixed thoroughly with 1.25 volumes of 100%molecular-grade ethanol and passed through a mirVana PARIS column insequential 700-μl aliquots. The column is washed following themanufacturer's protocol, and RNA is eluted in 105 μl of elution buffer(95° C.). A total of 1.5 μl of the eluate is quantified by Nanodrop.

Example 11 Measurement of miRNA Levels in RNA from Plasma and Serumusing qRT-PCR

A fixed volume of 1.67 μl of RNA solution from about ˜80 μl-eluate fromRNA isolation of a given sample is used as input into the reversetranscription (RT) reaction. For samples in which RNA is isolated from a400-μl plasma or serum sample, for example, 1.67 μl of RNA solutionrepresents the RNA corresponding to (1.67/80)×400=8.3 μl plasma orserum. For generation of standard curves of chemically synthesized RNAoligonucleotides corresponding to known miRNAs, varying dilutions ofeach oligonucleotide are made in water such that the final input intothe RT reaction has a volume of 1.67 μl. Input RNA is reversetranscribed using the TaqMan miRNA Reverse Transcription Kit andmiRNA-specific stem-loop primers (Applied BioSystems) in a small-scaleRT reaction comprised of 1.387 μl of H2O, 0.5 μl of 10×Reverse-Transcription Buffer, 0.063 μl of RNase-Inhibitor (20 units/μl),0.05 μl of 100 mM dNTPs with dTTP, 0.33 μl of MultiscribeReverse-Transcriptase, and 1.67 μl of input RNA; components other thanthe input RNA can be prepared as a larger volume master mix, using aTetrad2 Peltier Thermal Cycler (BioRad) at 16° C. for 30 min, 42° C. for30 min and 85° C. for 5 min. Real-time PCR is carried out on an AppliedBioSystems 7900HT thermocycler at 95° C. for 10 min, followed by 40cycles of 95° C. for 15 s and 60° C. for 1 min. Data is analyzed withSDS Relative Quantification Software version 2.2.2 (AppliedBioSystems.), with the automatic Ct setting for assigning baseline andthreshold for Ct determination.

The protocol can also be modified to include a preamplification step,such as for detecting miRNA. A 1.25-μl aliquot of undiluted RT productis combined with 3.75 μl of Preamplification PCR reagents [comprised,per reaction, of 2.5 μl of TaqMan PreAmp Master Mix (2×) and 1.25 μl of0.2× TaqMan miRNA Assay (diluted in TE)] to generate a 5.0-μlpreamplification PCR, which is carried out on a Tetrad2 Peltier ThermalCycler (BioRad) by heating to 95° C. for 10 min, followed by 14 cyclesof 95° C. for 15 s and 60° C. for 4 min. The preamplification PCRproduct is diluted (by adding 20 μl of H2O to the 5-μl preamplificationreaction product), following which 2.25 μl of the diluted material isintroduced into the real-time PCR and carried forward as described.

Example 12 Extracting microRNA from Vesicles

MicroRNA is extracted from vesicles isolated from patient samples asdescribed herein. See, e.g., Example 6. Methods for isolation andconcentration of vesicles are presented herein. The methods in thisExample can also be used to isolate microRNA from patient sampleswithout first isolating vesicles.

Protocol Using Trizol

This protocol uses the QIAzol Lysis Reagent and RNeasy Midi Kit fromQiagen Inc., Valencia Calif. to extract microRNA from concentratedvesicles. The steps of the method comprise:

1. Add 2 μl of RNase A to 50 μl of vesicle concentrate, incubate at 37°C. for 20 min.2. Add 700 μl of QIAzol Lysis Reagent, vortex 1 minute. Spike sampleswith 25 fmol/μL of C. elegans microRNA (1 μL) after the addition ofQIAzol, making a 75 fmol/μL spike in for each total sample (3 aliquotscombined).

3. Incubate at 55° C. for 5 min.

4. Add 140 μl chloroform and shake vigorously for 15 sec.

5. Cool on ice for 2-3 min. 6. Centrifuge @ 12,000×g at 4° C. for 15min.

7. Transfer aqueous phase (300 μL) to a new tube and add 1.5 volumes of100% EtOH (i.e., 450 μL).8. Pipet up to 4 ml of sample into an RNeasy Midi spin column in a 15 mlcollection tube (combining lysis from 3 50 μl of concentrate)9. Spin at 2700×g for 5 min at room temperature.10. Discard flowthrough from the spin.11. Add 1 ml of Buffer RWT to column and centrifuge at 2700×g for 5 minat room temperature. Do not use Buffer RW1 supplied in the Midi kit.Buffer RW1 can wash away miRNA. Buffer RWT is supplied in the Mini kitfrom Qiagen Inc.12. Discard flowthrough.13. Add 1 ml of Buffer RPE onto the column and centrifuge at 2700×g for2 min at room temperature.14. Repeat steps 12 and 13.16. Place column into a new 15 ml collection tube and add 150 μl ElutionBuffer. Incubate at room temperature for 3 min.17. Centrifuge at 2700×g for 3 min at room temperature.18. Vortex the sample and transfer to 1.7 mL tube. Store the extractedsample at −80° C.

Modified Trizol Protocol

1. Add Epicentre RNase A to final concentration of 229 μg/ml(Epicentre®, an Illumina® company, Madison, Wis.). (For example, to 150ul of concentrate, add 450 μl PBS and 28.8 μl Epicentre Rnase A [5μg/μl].) Vortex briefly. Incubate for 20 min at 37° C. Aliquot “babies”in increments of 100 μl using reverse pipetting.2. Set temperature on centrifuge to 4° C.3. Add 750 μl of Trizol LS to each 100 μl sample and immediately vortex.5. Incubate on benchtop at room temperature (RT) for 5 mins.6. Vortex all samples for 30 min. at 1400 rpm at RT in the MixMate.While vortexing, add BCP phase separation agent to the plate.7. Briefly centrifuge tubes. Transfer the sample to the collectionmicrotube rack.8. Add 150 μl BCP to the samples in the plate. Cap the plate and shakevigorously for 15 sec.

9. Incubate at RT for 3 min.

10. Centrifuge at 6,000×g at 4° C. for 15 min. Reset centrifugetemperature to 24° C. (RT).11. Add 500 μl 100% EtOH to the appropriate wells of a new S-block.Transfer 200 μl aqueous phase to new S-block, mix the aqueous/EtOH bypipetting 10×.12. Briefly centrifuge.13. Place an RNeasy 96 (Qiagen, Inc., Valencia, Calif.) plate on top ofa new S-block. Pipette the aqueous/EtOH sample mixture into the wells ofthe RNeasy 96 plate. Seal the RNeasy 96 plate with AirPore tape.14. Spin at 6000 rpm (5600×g) for 4 min at RT. Avoid temps below 24° C.15. Empty the S-block by discarding the flowthrough and remove theAirPore tape.14. Add 700 μl of Buffer RWT to the plate, seal with AirPore tape, andcentrifuge at 6,000 rpm for 4 min at RT. Empty the S-block and removethe AirPore tape.15. Add 500 μl of Buffer RPE to the plate, seal with AirPore tape, andcentrifuge at 6,000 rpm for 4 min at RT. Empty the S-block and removethe AirPore tape.16. Add another 500 μl of Buffer RPE to the plate, seal with AirPoretape, and centrifuge at 6,000 rpm for 10 min at RT. Empty the S-blockand remove the AirPore tape.17. Place the Rneasy 96 plate on top of a clean elution microtube rack.Pipet 30 μl of RNase-free water onto the columns of the Rneasy 96 plate.Seal with AirPore tape.18. Allow water to sit on column for 5 min.19. Centrifuge column for 4 min at 6,000 rpm to elute RNA. Cap themicrotubes with elution microtube caps. Pool babies together.

20. Store @−80° C.

Protocol using MagMax

This protocol uses the MagMAX™ RNA Isolation Kit from AppliedBiosystems/Ambion, Austin, Tex. to extract microRNA from concentratedvesicles. The steps of the method comprise:

1. Add 700 ml of QIAzol Lysis Reagent and vortex 1 minute.2. Incubate on benchtop at room temperature for 5 min.3. Add 140 μl chloroform and shake vigorously for 15 sec.4. Incubate on benchtop for 2-3 min.

5. Centrifuge at 12,000×g at 4° C. for 15 min.

6. Transfer aqueous phase to a deep well plate and add 1.25 volumes of100% Isopropanol.7. Shake MagMAX™ binding beads well. Pipet 10 μl of RNA binding beadsinto each well.8. Gather two elution plates and two additional deep well plates.9. Label one elution plate “Elution” and the other “Tip Comb.”10. Label one deep well as “1st Wash 2” and the other as “2nd Wash 2.”11. Fill both Wash 2 deep well plates with 150 μl of Wash 2, being sureto add ethanol to wash beforehand. Fill in the same number of wells asthere are samples.12. Select the appropriate collection program on the MagMax ParticleProcessor.13. Press start and load each appropriate plate.14. Transfer samples to microcentrifuge tubes.15. Vortex and store at −80° C. Residual beads will be seen in sample.

Example 13 MicroRNA Arrays

MicroRNA levels in a sample can be analyzed using an array format,including both high density and low density arrays. Array analysis canbe used to discover differentially expressed in a desired setting, e.g.,by analyzing the expression of a plurality of miRs in two samples andperforming a statistical analysis to determine which ones aredifferentially expressed between the samples and can therefore be usedin a biosignature. The arrays can also be used to identify a presence orlevel of one or more microRNAs in a single sample in order tocharacterize a phenotype by identifying a biosignature in the sample.This Example describes commercially available systems that are used tocarry out the methods of the invention.

TaqMan Low Density Array

TaqMan Low Density Array (TLDA) miRNA cards are used to compareexpression of miRNA in various sample groups as desired. The miRNA arecollected and analyzed using the TaqMan® MicroRNA Assays and Arrayssystems from Applied Biosystems, Foster City, Calif. Applied BiosystemsTaqMan® Human MicroRNA Arrays are used according to the Megaplex™ PoolsQuick Reference Card protocol supplied by the manufacturer.

Exiqon mIRCURY LNA microRNA

The Exiqon miRCURY LNA™ Universal RT microRNA PCR Human Panels I and II(Exiqon, Inc, Woburn, Mass.) are used to compare expression of miRNA invarious sample groups as desired. The Exiqon 384 well panels include 750miRs. Samples are normalized to control primers towards synthetic RNAspike-in from Universal cDNA synthesis kit (UniSp6 CP). Results werenormalized to inter-plate calibrator probes.

With either system, quality control standards are implemented.Normalized values for each probe across three data sets for eachindication are averaged. Probes with an average CV % higher than 20% arenot used for analysis. Results are subjected to a paired t-test to finddifferentially expressed miRs between two sample groups. P-values arecorrected with a Benjamini and Hochberg false-discovery rate test.Results are analyzed using GeneSpring software (Agilent Technologies,Inc., Santa Clara, Calif.).

Example 14 MicroRNA Profiles in Vesicles

Vesicles were collected by ultracentrifugation from 22Rv1, LNCaP, Vcapand normal plasma (pooled from 16 donors) as described in Examples 1-3.RNA was extracted using the Exiqon miR isolation kit (Cat. Nos. 300110,300111). Equals amounts of vesicles (30 μg) were used as determined byBCA assay.

Equal volumes (5 μl) were put into a reverse-transcription reaction formicroRNA. The reverse-transcriptase reactions were diluted in 81 μl ofnuclease-free water and then 9 μl of this solution was added to eachindividual miR assay. MiR-629 was found to only be expressed in PCa(prostate cancer) vesicles and was virtually undetectable in normalplasma vesicles. MiR-9 was found to be highly overexpressed (˜704 foldincrease over normal as measured by copy number) in all PCa cell lines,and has very low expression in normal plasma vesicles.

Example 15 MicroRNA Profiles of Magnetic EpCam-Captured Vesicles

The bead-bound vesicles of Example 7 were placed in QIAzol™ LysisReagent (Qiagen Cat. #79306). An aliquot of 125 fmol of C. elegansmiR-39 was added. The RNA was isolated using the Qiagen miRneasy™ kit,(Cat. #217061), according to the manufacturer's instructions, and elutedin 30 ul RNAse free water.

10 μl of the purified RNA was placed into a pre-amplification reactionfor miR-9, miR-141 and miR-629 using a Veriti 96-well thermocycler. A1:5 dilution of the pre-amplification solution was used to set up aqRT-PCR reaction for miR9 (ABI 4373285), miR-141 (ABI 4373137) andmiR-629 (ABI 4380969) as well as c. elegans miR-39 (ABI 4373455). Theresults were normalized to the c. elegans results for each sample.

Example 16 MicroRNA Profiles of CD9-Captured Vesicles

CD9 coated Dynal beads (Invitrogen, Carlsbad, Calif.) were used insteadof EpCam coated beads as in Example 15. Vesicles from prostate cancerpatients, LNCaP, or normal purified vesicles were incubated with the CD9coated beads and the RNA isolated as described in Example 15. Theexpression of miR-21 and miR-141 was detected by qRT-PCR and the resultsdepicted in FIG. 6.

Example 17 Isolation of Vesicles Using a Filtration Module

Six mL of PBS is added to 1 mL of plasma. The sample is then put througha 1.2 micron (μm) Pall syringe filter directly into a 100 kDa MWCO(Millipore, Billerica, Mass.), 7 ml column with a 150 kDa MWCO (Pierce®,Rockford, Ill.), 15 ml column with a 100 kDa MWCO (Millipore, Billerica,Mass.), or 20 ml column with a 150 kDa MWCO (Pierce®, Rockford, Ill.).

The tube is centrifuged for between 60 to 90 minutes until the volume isabout 250 μl. The retentate is collected and PBC added to bring thesample up to 300 μl. Fifty μl of the sample is then used for furthervesicle analysis, such as further described in the examples below.

Example 18 Multiplex Analysis of Vesicles Isolated with Filters

The vesicle samples obtained using methods as described in Example 17are used in multiplexing assays as described herein. See, e.g., Examples23-24 below. The capture antibodies are CD9, CD63, CD81, PSMA, PCSA,B7H3, and EpCam. The detection antibodies are for biomarkers CD9, CD81,and CD63 or B7H3 and EpCam.

Example 19 Flow Cytometry Analysis of Vesicles

Purified plasma vesicles are assayed using the MoFlo XDP (BeckmanCoulter, Fort Collins, Colo., USA) and the median fluorescent intensityanalyzed using the Summit 4.3 Software (Beckman Coulter). Vesicles arelabeled directly with antibodies, or beads or microspheres (e.g.,magnetic, polystyrene, including BD FACS 7-color setup, catalog no.335775) can be incorporated. Vesicles can be detected with bindingagents against the following vesicle antigens: CD9 (Mouse anti-humanCD9, MAB1880, R&D Systems, Minneapolis, Minn., USA), PSM (Mouseanti-human PSM, sc-73651, Santa Cruz, Santa Cruz, Calif., USA), PCSA(Mouse anti-human Prostate Cell Surface Antigen, MAB4089, Millipore,Mass., USA), CD63 (Mouse anti-human CD63, 556019, BD Biosciences, SanJose, Calif., USA), CD81 (Mouse anti-human CD81, 555675, BD Biosciences,San Jose, Calif., USA) B7-H3 (Goat anti-human B7-H3, AF1027, R&DSystems, Minneapolis, Minn., USA), EpCAM (Mouse anti-human EpCAM,MAB9601, R&D Systems, Minneapolis, Minn., USA). Vesicles can be detectedwith fluorescently labeled antibodies against the desired vesicleantigens. For example, FITC, phycoerythrin (PE) and Cy7 are commonlyused to label the antibodies.

To capture the antibodies with multiplex microspheres, the microspherescan be obtained from Luminex (Austin, Tex., USA) and conjugated to thedesired antibodies using micros using Sulfo-NHS and EDC obtained fromPierce Thermo (Cat. No. 24510 and 22981, respectively, Rockford, Ill.,USA).

Purified vesicles (10 ug/ml) are incubated with 5,000 microspheres forone hour at room temperature with shaking. The samples are washed inFACS buffer (0.5% FBS/PBS) for 10 minutes at 1700 rpms. The detectionantibodies are incubated at the manufacturer's recommendedconcentrations for one hour at room temperature with shaking. Followinganother wash with FACS buffer for 10 minutes at 1700 rpms, the samplesare resuspended in 100 ul FACS buffer and run on the FACS machine.

Further when using microspheres to detect vesicles, the labeled vesiclescan be sorted according to their detection antibody content intodifferent tubes. For example, using FITC or PE labeled microspheres, afirst tube contains the population of microspheres with no detectors,the second tube contains the population with PE detectors, the thirdtube contains the population with FITC detectors, and the fourth tubecontains the population with both PE and FITC detectors. The sortedvesicle populations can be further analyzed, e.g., by examining payloadsuch as mRNA, microRNA or protein content.

FIG. 7 shows separation and identification of vesicles using the MoFloXDP. In this set of experiments, there were about 3000 trigger eventswith just buffer (i.e. particulates about the size of a large vesicle).There were about 46,000 trigger events with unstained vesicles (43,000vesicles of sufficient size to scatter the laser). There were 500,000trigger events with stained vesicles. Vesicles were detected usingdetection agents for tetraspanins CD9, CD63, and CD81 all labeled withFITC, The smaller vesicles can be detected when they are stained withdetection agents.

Physical isolation by sorting of specific populations of vesiclesfacilitates additional studies such as microRNA analysis on thepartially or wholly purified vesicle populations.

Example 20 Antibody Detection of Vesicles

Vesicles in a patient sample are assessed using antibody-coated beads todetect the vesicles in the sample using techniques as described herein.The following general protocol is used:

-   -   a. Blood is drawn from a patient at a point of care (e.g.,        clinic, doctor's office, hospital).    -   b. The plasma fraction of the blood is used for further        analysis.    -   c. To remove large particles and isolate a vesicle containing        fraction, the plasma sample is filtered, e.g., with a 0.8 or 1.2        micron (μm) syringe filter, and then passed through a size        exclusion column, e.g., with a 150 kDa molecular weight cut off.        A general schematic is shown in FIG. 8A. Filtration may be        preferable to ultracentrifugation, as illustrated in FIG. 8B.        Without being bound by theory, high-speed centrifugation may        remove protein targets weakly anchored in the membrane as        opposed to the tetraspanins which are more solidly anchored in        the membrane, and may reduce the cell specific targets in the        vesicle, which would then not be detected in subsequent analysis        of the biosignature of the vesicle.    -   d. The vesicle fraction is incubated with beads conjugated with        a “capture” antibody to a marker of interest. The captured        vesicles are then tagged with labeled “detection” antibodies,        e.g., phycoerythrin or FITC conjugated antibodies. The beads can        be labeled as well.    -   e. Captured and tagged vesicles in the sample are detected.        Fluorescently labeled beads and detection antibodies can be        detected as shown in FIG. 8C. Use of the labeled beads and        labeled detection antibodies allows assessment of beads with        vesicles bound thereto by the capture antibody.    -   f. Data is analyzed. A threshold can be set for the median        fluorescent intensity (MFI) of a particular capture antibody. A        reading for that capture antibody above the threshold can        indicate a certain phenotype. As an illustrative example, an MFI        above the threshold for a capture antibody directed to a cancer        marker can indicate the presense of cancer in the patient        sample.

In FIG. 8, the beads 816 flow through a capillary 811. Use of duallasers 812 at different wavelengths allows separate detection atdetector 813 of both the capture antibody 818 from the fluorescentsignal derived from the bead, as well as the median fluorescentintensity (MFI) resulting from the labeled detection antibodies 819. Useof labeled beads conjugated to different capture antibodies of interest,each bead labeled with a different fluor, allows for multiplex analysisof different vesicle 817 populations in a single assay as shown. Laser 1815 allows detection of bead type (i.e., the capture antibody) and Laser2 814 allows measurement of detector antibodies, which can includegeneral vesicle markers such as tetraspanins including CD9, CD63 andCD81. Use of different populations of beads and lasers allowssimultaneous multiplex analysis of many different populations ofvesicles in a single assay.

Example 21 Detection of Prostate Cancer

High quality training set samples were obtained from commercialsuppliers. The samples comprised plasma from 42 normal prostate, 42 PCaand 15 BPH patients. The PCa samples included 4 stage III and theremainder state II. The samples were blinded until all laboratory workwas completed.

The vesicles from the samples were obtained by filtration to eliminateparticles greater than 1.5 microns, followed by column concentration andpurification using hollow fiber membrane tubes. The samples wereanalyzed using a multiplexed bead-based assay system as described above.

Antibodies to the following proteins were analyzed:

-   -   a. General Vesicle (MV) markers: CD9, CD81, and CD63    -   b. Prostate MV markers: PCSA    -   c. Cancer-Associated MV markers: EpCam and B7H3

Samples were required to pass a quality test as follows: if multiplexedmedian fluorescence intensity (MFI) PSCA+MFI B7H3+MFI EpCam<200 thensample fails due to lack of signal above background. In the trainingset, six samples (three normals and three prostate cancers) did notachieve an adequate quality score and were excluded. An upper limit onthe MFI was also established as follows: if MFI of EpCam is >6300 thentest is over the upper limit score and samples are deemed not cancer(i.e., “negative” for purposes of the test).

The samples were classified according to the result of MFI scores forthe six antibodies to the training set proteins, wherein the followingconditions must be met for the sample to be classified as PCa positive:

-   -   a. Average MFI of General MV markers>1500    -   b. PCSA MFI>300    -   c. B7H3 MFI>550    -   d. EpCam MFI between 550 and 6300

Using the 84 normal and PCa training data samples, the test was found tobe 98% sensitive and 95% specific for PCa vs normal samples. See FIG.9A. The increased MFI of the PCa samples compared to normals is shown inFIG. 9B. Compared to PSA and PCA3 testing, the PCa Test presented inthis Example can result in saving ˜220 men without PCa in every 1000normal men screened from having an unnecessary biopsy.

Example 22 Microsphere Vesicle Prostate Cancer Assay Protocol

In this example, the vesicle PCa test is a microsphere based immunoassayfor the detection of a set of protein biomarkers present on the vesiclesfrom plasma of patients with prostate cancer. The test employs specificantibodies to the following protein biomarkers: CD9, CD59, CD63, CD81,PSMA, PCSA, B7H3 and EpCAM. After capture of the vesicles by antibodycoated microspheres, phycoerythrin-labeled antibodies are used for thedetection of vesicle specific biomarkers. Depending on the level ofbinding of these antibodies to the vesicles from a patient's plasma adetermination of the presence or absence of prostate cancer is made.

Vesicles are isolated as described above.

Microspheres

Specific antibodies are conjugated to microspheres (Luminex) after whichthe microspheres are combined to make a Microsphere Master Mixconsisting of L100-C105-01; L100-C115-01; L100-C119-01; L100-C120-01;L100-C122-01; L100-C124-01; L100-C135-01; and L100-C175-01. xMAP®Classification Calibration Microspheres L100-CAL1 (Luminex) are used asinstrument calibration reagents for the Luminex LX200 instrument. xMAP®Reporter Calibration Microspheres L100-CAL2 (Luminex) are used asinstrument reporter calibration reagents for the Luminex LX200instrument. xMAP® Classification Control Microspheres L100-CON1(Luminex) are used as instrument control reagents for the Luminex LX200instrument. xMAP Reporter Control Microspheres L100-CON2 (Luminex) andare used as reporter control reagents for the Luminex LX200 instrument.

Capture Antibodies

The following antibodies are used to coat Luminex microspheres for usein capturing certain populations of vesicles by binding to theirrespective protein targets on the vesicles in this Example: a. Mouseanti-human CD9 monoclonal antibody is an IgG2b used to coat microsphereL100-C105 to make *EPCLMACD9-C105; b. Mouse anti-human PSMA monoclonalantibody is an IgG1 used to coat microsphere L100-C115 to makeEPCLMAPSMA-C115; c. Mouse anti-human PCSA monoclonal antibody is an IgG1used to coat microsphere L100-C119 to make EPCLMAPCSA-C119; d. Mouseanti-human CD63 monoclonal antibody is an IgG1 used to coat microsphereL100-C120 to make EPCLMACD63-C120; e. Mouse anti-human CD81 monoclonalantibody is an IgG1 used to coat microsphere L100-C124 to makeEPCLMACD81-C124; f. Goat anti-human B7-H3 polyclonal antibody is an IgGpurified antibody used to coat microsphere L100-C125 to makeEPCLGAB7-H3-C125; and g. Mouse anti-human EpCAM monoclonal antibody isan IgG2b purified antibody used to coat microsphere L100-C175 to makeEPCLMAEpCAM-C175.

Detection Antibodies

The following phycoerythrin (PE) labeled antibodies are used asdetection probes in this assay: a. EPCLMACD81PE: Mouse anti-human CD81PE labeled antibody is an IgG1 antibody used to detect CD81 on capturedvesicles; b. EPCLMACD9PE: Mouse anti-human CD9 PE labeled antibody is anIgG1 antibody used to detect CD9 on captured vesicles; c. EPCLMACD63PE:Mouse anti-human CD63 PE labeled antibody is an IgG1 antibody used todetect CD63 on captured vesicles; d. EPCLMAEpCAMPE: Mouse anti-humanEpCAM PE labeled antibody is an IgG1 antibody used to detect EpCAM oncaptured vesicles; e. EPCLMAPSMAPE: Mouse anti-human PSMA PE labeledantibody is an IgG1 antibody used to detect PSMA on captured vesicles;f. EPCLMACD59PE: Mouse anti-human CD59 PE labeled antibody is an IgG1antibody used to detect CD59 on captured vesicles; and g. EPCLMAB7-H3PE:Mouse anti-human B7-H3 PE labeled antibody is an IgG1 antibody used todetect B7-H3 on captured vesicles.

Reagent Preparation

Antibody Purification:

The following antibodies in Table 12 are received from vendors andpurified and adjusted to the desired working concentrations according tothe following protocol.

TABLE 12 Antibodies for PCa Assay Antibody Use EPCLMACD9 Coating ofmicrospheres for vesicle capture EPCLMACD63 Coating of microspheres forvesicle capture EPCLMACD81 Coating of microspheres for vesicle captureEPCLMAPSMA Coating of microspheres for vesicle capture EPCLGAB7-H3Coating of microspheres for vesicle capture EPCLMAEpCAM Coating ofmicrospheres for vesicle capture EPCLMAPCSA Coating of microspheres forvesicle capture EPCLMACD81PE PE coated antibody for vesicle biomarkerdetection EPCLMACD9PE PE coated antibody for vesicle biomarker detectionEPCLMACD63PE PE coated antibody for vesicle biomarker detectionEPCLMAEpCAMPE PE coated antibody for vesicle biomarker detectionEPCLMAPSMAPE PE coated antibody for vesicle biomarker detectionEPCLMACD59PE PE coated antibody for vesicle biomarker detectionEPCLMAB7-H3PE PE coated antibody for vesicle biomarker detection

Antibody Purification Protocol:

Antibodies are purified using Protein G resin from Pierce (Protein Gspin kit, prod #89979). Micro-chromatography columns made from filteredP-200 tips are used for purification.

One hundred μl of Protein G resin is loaded with 100 μl buffer from thePierce kit to each micro column. After waiting a few minutes to allowthe resin to settle down, air pressure is applied with a P-200 Pipettmanto drain buffer when needed, ensuring the column is not let to dry. Thecolumn is equilibrated with 0.6 ml of Binding Buffer (pH 7.4, 100 mMPhosphate Buffer, 150 mM NaCl; (Pierce, Prod #89979). An antibody isapplied to the column (<1 mg of antibody is loaded on the column). Thecolumn is washed with 1.5 ml of Binding Buffer. Five tubes (1.5 ml microcentrifuge tubes) are prepared and 10 μl of neutralization solution(Pierce, Prod #89979) is applied to each tube. The antibody is elutedwith the elution buffer from the kit to each of the five tubes, 100 ulfor each tube (for a total of 500 μl). The relative absorbance of eachfraction is measured at 280 nm using Nanodrop (Thermo scientific,Nanodrop 1000 spectrophotometer). The fractions with highest OD readingare selected for downstream usage. The samples are dialyzed against 0.25liters PBS buffer using Pierce Slide-A-Lyzer Dialysis Cassette (Pierce,prod 66333, 3 KDa cut off). The buffer is exchanged every 2 hours forminimum three exchanges at 4° C. with continuous stirring. The dialyzedsamples are then transferred to 1.5 ml microcentrifuge tubes, and can belabeled and stored at 4° C. (short term) or −20° C. (long term).

Microsphere Working Mix Assembly:

A microsphere working mix MWM101 includes the first four rows ofantibody, microsphere and coated microsphere of Table 13.

TABLE 13 Antibody-Microsphere Combinations Antibody Microsphere CoatedMicrosphere EPCLMACD9 L100-C105 EPCLMACD9-C105 EPCLMACD63 L100-C120EPCLMACD63-C120 EPCLMACD81 L100-C124 EPCLMACD81-C124 EPCLMAPSMAL100-C115 EPCLMAPSMA-C115 EPCLGAB7-H3 L100-C125 EPCLGAB7-H3-C125bEPCLMAEpCAM L100-C175 EPCLMAEpCAM-C175 EPCLMAPCSA L100-C119EPCLMAPCSA-C119

Microspheres are coated with their respective antibodies as listed aboveaccording to the following protocol.

Protocol for Two-Step Carbodiimide Coupling of Protein to CarboxylatedMicrospheres:

The microspheres should be protected from prolonged exposure to lightthroughout this procedure. The stock uncoupled microspheres areresuspended according to the instructions described in the ProductInformation Sheet provided with the microspheres (xMAP technologies,MicroPlex™ Microspheres). Five×106 of the stock microspheres aretransferred to a USA Scientific 1.5 ml microcentrifuge tube. The stockmicrospheres are pelleted by microcentrifugation at ≧8000×g for 1-2minutes at room temperature. The supernatant is removed and the pelletedmicrospheres are resuspended in 100 μl of dH2O by vortex and sonicationfor approximately 20 seconds. The microspheres are pelleted bymicrocentrifugation at ≧8000×g for 1-2 minutes at room temperature. Thesupernatant is removed and the washed microspheres are resuspended in 80μl of 100 mM Monobasic Sodium Phosphate, pH 6.2 by vortex and sonication(Branson 1510, Branson UL Trasonics Corp.) for approximately 20 seconds.Ten μl of 50 mg/ml Sulfo-NHS (Thermo Scientific, Cat#24500) (diluted indH2O) is added to the microspheres and is mixed gently by vortex. Ten μlof 50 mg/ml EDC (Thermo Scientific, Cat#25952-53-8) (diluted in dH20) isadded to the microspheres and gently mixed by vortexing. Themicrospheres are incubated for 20 minutes at room temperature withgentle mixing by vortex at 10 minute intervals. The activatedmicrospheres are pelleted by microcentrifugation at ≧8000×g for 1-2minutes at room temperature. The supernatant is removed and themicrospheres are resuspended in 250 μl of 50 mM MES, pH 5.0 (MES, Sigma,Cat# M2933) by vortex and sonication for approximately 20 seconds. (OnlyPBS-1% BSA+Azide (PBS-BN) ((Sigma (P3688-10PAK+0.05% NaAzide (S8032)))should be used as assay buffer as well as wash buffer.). Themicrospheres are then pelleted by microcentrifugation at ≧8000×g for 1-2minutes at room temperature.

The supernatant is removed and the microspheres are resuspended in 250μl of 50 mM MES, pH 5.0 (MES, Sigma, Cat# M2933) by vortex andsonication for approximately 20 seconds. (Only PBS-1% BSA+Azide (PBS-BN)((Sigma (P3688-10PAK+0.05% NaAzide (S8032))) should be used as assaybuffer as well as wash buffer.). The microspheres are then pelleted bymicrocentrifugation at ≧8000×g for 1-2 minutes at room temperature, thuscompleting two washes with 50 mM MES, pH 5.0.

The supernatant is removed and the activated and washed microspheres areresuspended in 100 μl of 50 mM MES, pH 5.0 by vortex and sonication forapproximately 20 seconds. Protein in the amount of 125, 25, 5 or 1 μg isadded to the resuspended microspheres. (Note: Titration in the 1 to 125μg range can be performed to determine the optimal amount of protein perspecific coupling reaction.). The total volume is brought up to 500 μlwith 50 mM MES, pH 5.0. The coupling reaction is mixed by vortex and isincubated for 2 hours with mixing (by rotating on Labquake rotator,Barnstead) at room temperature. The coupled microspheres are pelleted bymicrocentrifugation at ≧8000×g for 1-2 minutes at room temperature. Thesupernatant is removed and the pelleted microspheres are resuspended in500 μL of PBS-TBN by vortex and sonication for approximately 20 seconds.(Concentrations can be optimized for specific reagents, assayconditions, level of multiplexing, etc. in use.).

The microspheres are incubated for 30 minutes with mixing (by rotatingon Labquake rotator, Barnstead) at room temperature. The coupledmicrospheres are pelleted by microcentrifugation at ≧8000×g for 1-2minutes at room temperature. The supernatant is removed and themicrospheres are resuspended in 1 ml of PBS-TBN by vortex and sonicationfor approximately 20 seconds. (Each time there is the addition ofsamples, detector antibody or SA-PE the plate is covered with a sealerand light blocker (such as aluminum foil), placed on the orbital shakerand set to 900 for 15-30 seconds to re-suspend the beads. Following thatthe speed should be set to 550 for the duration of the incubation.).

The microspheres are pelleted by microcentrifugation at ≧8000×g for 1-2minutes. The supernatant is removed and the microspheres are resuspendedin 1 ml of PBS-TBN by vortex and sonication for approximately 20seconds. The microspheres are pelleted by microcentrifugation at ≧8000×gfor 1-2 minutes (resulting in a total of two washes with 1 ml PBS-TBN).

Protocol for Microsphere Assay:

The preparation for multiple phycoerythrin detector antibodies is usedas described in Example 4. One hundred μl is analyzed on the Luminexanalyzer (Luminex 200, xMAP technologies) according to the system manual(High PMT setting).

Decision Tree:

A decision tree as in FIG. 10 is used to assess the results from themicrosphere assay to determine if a subject has cancer. Threshold limitson the MFI is established and samples classified according to the resultof MFI scores for the antibodies, to determine whether a sample hassufficient signal to perform analysis (e.g., is a valid sample foranalysis or an invalid sample for further analysis, in which case asecond patient sample may be obtained) and whether the sample is PCapositive. FIG. 10 shows a decision tree using the MFI obtained withPCSA, PSMA, B7-H3, CD9, CD81 and CD63. A sample is classified asindeterminate if the MFI is within the standard deviation of thepredetermined threshold (TH). In this case, a second patient sample canbe obtained. For validation, the sample must have sufficient signal whencapturing vesicles with the individual tetraspanins and labeling withall tetraspanins. A sample that passes validation is called positive ifeither of the prostate-specific markers (PSMA or PCSA) is consideredpositive, and the cancer marker (B7-H3) is also considered positive.

Results: See Example 23.

Example 23 Microsphere Vesicle PCa Assay Performance

In this example, the vesicle PCa test is a microsphere based immunoassayfor the detection of a set of protein biomarkers present on the vesiclesfrom plasma of patients with prostate cancer. The test is performedsimilarly to that of Example 22 with modifications indicated below.

The test uses a multiplexed immunoassay designed to detect circulatingmicrovesicles. The test uses PCSA, PSMA and B7H3 to capture themicrovesicles present in patient samples such as plasma and uses CD9,CD81, and CD63 to detect the captured microvesicles. The output of thisassay is the median fluorescent intensity (MFI) that results from theantibody capture and fluorescently labeled antibody detection ofmicrovesicles that contain both the individual capture protein and thedetector proteins on the microvesicle. A sample is “POSITIVE” by thistest if the MFI levels of PSMA or PCSA, and B7H3 protein-containingmicrovesicles are above the empirically determined threshold. A methodfor determining the threshold is presented in Example 33 ofInternational Patent Application Serial No. PCT/US2011/031479, entitled“Circulating Biomarkers for Disease” and filed Apr. 6, 2011, whichapplication is incorporated by reference in its entirety herein. Asample is determined to be “NEGATIVE” if any one of these twomicrovesicle capture categories exhibit an MFI level that is below theempirically determined threshold. Alternatively, a result of“INDETERMINATE” will be reported if the sample MFI fails to clearlyproduce a positive or negative result due to MFI values not meetingcertain thresholds or the replicate data showed too much statisticalvariation. A “NON-EVALUABLE” interpretation for this test indicates thatthis patient sample contained inadequate microvesicle quality foranalysis. See Example 33 of International Patent Application Serial No.PCT/US2011/031479 for a method to determine the empirically derivedthreshold values.

The test employs specific antibodies to the following proteinbiomarkers: CD9, CD59, CD63, CD81, PSMA, PCSA, and B7H3 as in Example22. Decision rules are set to determine if a sample is called positive,negative or indeterminate, as outlined in Table 14. See also Example 22.For a sample to be called positive the replicates must exceed all fourof the MFI cutoffs determined for the tetraspanin markers (CD9, CD63,CD81), prostate markers (PSMA or PCSA), and B7H3. Samples are calledindeterminate if both of the three replicates from PSMA and PCSA or anyof the three replicates from B7H3 antibodies span the cutoff MFI value.Samples are called negative if there is at least one of the tetraspaninmarkers (CD9, CD63, and CD81), prostate markers (PSMA or PCSA), B7H3that fall below the MFI cutoffs.

TABLE 14 MFI Parameter for Each Capture Antibody Tetraspanin MarkersProstate Markers Result (CD9, CD63, CD81) (PSMA, PCSA) B7H3Determination Average of all All replicates from All replicates from Ifall 3 are true, replicates from the either of the two B7H3 have a MFIthen the sample is three tetraspanins have prostate markers have >300called Positive a MFI >500 a MFI >350 for PCSA and >90 for PSMA Bothreplicate sets Any replicates If either are true, from either prostatefrom B7H3 have then the sample is marker have values values both abovecalled both above and below and below a MFI = indeterminate a MFI = 350for PCSA 300 and = 90 for PSMA All replicates from the All replicatesfrom All replicates from If any of the 3 are three tetraspanins haveeither of the two B7H3 have a MFI true, then the a MFI <500 prostatemarkers have <300 sample is called a MFI <350 for PCSA Negative, giventhe and <90 for PSMA sample doesn't qualify as indeterminate

The vesicle PCa test was compared to elevated PSA on a cohort of 296patients with or without PCa as confirmed by biopsy. An ROC curve of theresults is shown in FIG. 11. As shown, the area under the curve (AUC)for the vesicle PCa test was 0.94 whereas the AUC for elevated PSA onthe same samples was only 0.68. The PCa samples were likely found due toa high PSA value. Thus this population is skewed in favor of PSA,accounting for the higher AUC than is observed in a true clinicalsetting.

The vesicle PCa test was further performed on a cohort of 933 patientplasma samples. Results are summarized in Table 15:

TABLE 15 Performance of vesicle PCa test on 933 patient cohort TruePositive 409 True Negative 307 False Positive 50 False Negative 72Non-evaluable 63 Indeterminate 32 Total 933 Sensitivity 85% Specificity86% Accuracy 85% Non-evaluable Rate  8% Indeterminate Rate  5%

As shown in Table 15, the vesicle PCa test achieved an 85% sensitivitylevel at a 86% specificity level, for an accuracy of 85%. In contrast,PSA at a sensitivity of 85% had a specificity of about 55%, and PSA at aspecificity of 86% had a sensitivity of about 5%. FIG. 11. About 12% ofthe 933 samples were non-evaluable or indeterminate. Samples from thepatients could be recollected and re-evaluated. The vesicle PCa test hadan AUC of 0.92 for the 933 samples.

Example 24 Vesicle Protein Array to Detect Prostate Cancer

In this example, the vesicle PCa test is performed using a proteinarray, more specifically an antibody array, for the detection of a setof protein biomarkers present on the vesicles from plasma of patientswith prostate cancer. The array comprises capture antibodies specific tothe following protein biomarkers: CD9, CD59, CD63, CD81. Vesicles areisolated as described above, e.g., in Example 6. After filtration andisolation of the vesicles from plasma of men at risk for PCa, such asthose over the age of 50, the plasma samples are incubated with an arrayharboring the various capture antibodies. Depending on the level ofbinding of fluorescently labeled detection antibodies to PSMA, PCSA,B7H3 and EpCAM that bind to the vesicles from a patient's plasma thathybridize to the array, a determination of the presence or absence ofprostate cancer is made.

In a second array format, the vesicles are isolated from plasma andhybridized to an array containing CD9, CD59, CD63, CD81, PSMA, PCSA,B7H3 and EpCam. The captured vesicles are tagged with non-specificvesicle antibodies labeled with Cy3 and/or Cy5. The fluorescence isdetected. Depending on the pattern of binding, a determination of thepresence or absence of prostate cancer is made.

Example 25 Distinguishing BPH and PCa Using miR5

RNA from the plasma derived vesicles of nine normal male individuals andnine individuals with stage 3 prostate cancers were analyzed on theExiqon mIRCURY LNA microRNA PCR system panel. The Exiqon 384 well panelsmeasure 750 miRs. Samples were normalized to control primers towardssynthetic RNA spike-in from Universal cDNA synthesis kit (UniSp6 CP).Normalized values for each probe across three data sets for eachindication (BPH or PCa) were averaged. Probes with an average CV %higher than 20% were not used for analysis.

Analysis of the results revealed several microRNAs that were 2 fold ormore over-expressed in BPH samples compared to Stage 3 prostate cancersamples. These miRs include: hsa-miR-329, hsa-miR-30a, hsa-miR-335,hsa-miR-152, hsa-miR-151-5p, hsa-miR-200a and hsa-miR-145, as shown inTable 16:

TABLE 16 miRs overexpressed in BPH vs PCa Overexpressed in BPH v PCaFold Change hsa-miR-329 12.32 hsa-miR-30a 6.16 hsa-miR-335 6.00hsa-miR-152 4.73 hsa-miR-151-5p 3.16 hsa-miR-200a 3.16 hsa-miR-145 2.35

Example 26 miR-145 in Controls and PCa Samples

FIG. 12 illustrates a comparison of miR-145 in control and prostatecancer samples. RNA was collected as in Example 12. The controls includeCaucasians>75 years old and African Americans>65 years old with PSA<4ng/ml and a benign digital rectal exam (DRE). As seen in the figure,miR-145 was under expressed in PCa samples. miR-145 is useful foridentifying those with early/indolent PCa vs those with benign prostatechanges (e.g., BPH).

Example 27 miRs to Enhance Vesicle Diagnostic Assay Performance

As described herein, vesicles are concentrated in plasma patient samplesand assessed to provide a diagnostic, prognostic or theranostic readout.Vesicle analysis of patient samples includes the detection of vesiclesurface biomarkers, e.g., surface antigens, and/or vesicle payload,e.g., mRNAs and microRNAs, as described herein. The payload within thevesicles can be assessed to enhance assay performance. For example, FIG.13A illustrates a scheme for using miR analysis within vesicles toconvert false negatives into true positives, thereby improvingsensitivity. In this scheme, samples called negative by the vesiclesurface antigen analysis are further confirmed as true negatives or truepositives by assessing payload with the vesicles. Similarly, FIG. 13Billustrates a scheme for using miR analysis within vesicles to convertfalse positives into true negatives, thereby improving specificity. Inthis scheme, samples called positive by the vesicle surface antigenanalysis are further confirmed as true negatives or true positives byassessing payload with the vesicles.

A diagnostic test for prostate cancer includes isolating vesicles from ablood sample from a patient to detect vesicles indicative of thepresence or absence of prostate cancer. See, e.g., Examples 20-23. Theblood can be serum or plasma. The vesicles are isolated by capture with“capture antibodies” that recognize specific vesicle surface antigens.The surface antigens for the prostate cancer diagnostic assay includethe tetraspanins CD9, CD63 and CD81, which are generally present onvesicles in the blood and therefore act as general vesicle biomarkers,the prostate specific biomarkers PSMA and PCSA, and the cancer specificbiomarker B7H3. The capture antibodies are tethered to fluorescentlylabeled beads, wherein the beads are differentially labeled for eachcapture antibody. Captured vesicles are further highlighted usingfluorescently labeled “detection antibodies” to the tetraspanins CD9,CD63 and CD81. Fluorescence from the beads and the detection antibodiesis used to determine an amount of vesicles in the plasma sampleexpressing the surface antigens for the prostate cancer diagnosticassay. The fluorescence levels in a sample are compared to a referencelevel that can distinguish samples having prostate cancer. In thisExample, microRNA analysis is used to enhance the performance of thevesicle-based prostate cancer diagnostic assay.

FIG. 13C shows the results of detection of miR-107 in samples assessedby the vesicle-based prostate cancer diagnostic assay. FIG. 13D showsthe results of detection of miR-141 in samples assessed by thevesicle-based prostate cancer diagnostic assay. In the figure,normalized levels of the indicated miRs are shown on the Y axis for truepositives (TP) called by the vesicle diagnostic assay, true negatives(TN) called by the vesicle diagnostic assay, false positives (FP) calledby the vesicle diagnostic assay, and false negatives (FN) called by thevesicle diagnostic assay. As shown in FIG. 13C, the use of miR-107enhances the sensitivity of the vesicle assay by distinguishing falsenegatives from true negative (p=0.0008). Similarly, FIG. 13D also showsthat the use of miR-141 enhances the sensitivity of the vesicle assay bydistinguishing false negatives from true negative (p=0.0001). Results ofadding miR-141 are shown in Table 17. miR-574-3p performs similarly.

TABLE 17 Addition of miR-141 to vesicle-based test for PCa WithoutmiR-141 With miR-141 Sensitivity 85% 98% Specificity 86% 86%

In this Example, vesicles are detected via surface antigens that areindicative of prostate cancer, and the performance of the signature isfurther bolstered by examining miRs within the vesicles, i.e.,sensitivity is increased without negatively affecting specificity. Thisgeneral methodology can be extended for any setting in which vesiclesare profiled for surface antigens or other informative characteristic,then one or more additional biomarker is used to enhancecharacterization. Here, the one or more additional biomarkers are miRs.They could also comprise mRNA, soluble protein, lipids, carbohydratesand any other vesicle-associated biological entities that are useful forcharacterizing the phenotype of interest.

Example 28 Vesicle Isolation and Detection Methods

A number of technologies known to those of skill in the art can be usedfor isolation and detection of vesicles to carry out the methods of theinvention in addition to those described above. The following is anillustrative description of several such methods.

Glass Microbeads.

Available as VeraCode/BeadXpress from Illumina, Inc. San Diego, Calif.,USA. The steps are as follows:

-   -   1. Prepare the beads by direct conjugation of antibodies to        available carboxyl groups.    -   2. Block non specific binding sites on the surface of the beads.    -   3. Add the beads to the vesicle concentrate sample.    -   4. Wash the samples so that unbound vesicles are removed.    -   5. Apply fluorescently labeled antibodies as detection        antibodies which will bind specifically to the vesicles.    -   6. Wash the plate, so that the unbound detection antibodies are        removed.    -   7. Measure the fluorescence of the plate wells to determine the        presence the vesicles.

Enzyme Linked Immunosorbent Assay (ELISA).

Methods of performing ELISA are well known to those of skill in the art.The steps are generally as follows:

-   -   1. Prepare a surface to which a known quantity of capture        antibody is bound.    -   2. Block non specific binding sites on the surface.    -   3. Apply the vesicle sample to the plate.    -   4. Wash the plate, so that unbound vesicles are removed.    -   5. Apply enzyme linked primary antibodies as detection        antibodies which also bind specifically to the vesicles.    -   6. Wash the plate, so that the unbound antibody-enzyme        conjugates are removed.    -   7. Apply a chemical which is converted by the enzyme into a        color, fluorescent or electrochemical signal.    -   8. Measure the absorbency, fluorescence or electrochemical        signal (e.g., current) of the plate wells to determine the        presence and quantity of vesicles.

Electrochemiluminescence Detection Arrays.

Available from Meso Scale Discovery, Gaithersburg, Md., USA:

-   -   1. Prepare plate coating buffer by combining 5 mL buffer of        choice (e.g. PBS, TBS, HEPES) and 75 μL of 1% Triton X-100        (0.015% final).    -   2. Dilute capture antibody to be coated.    -   3. Prepare 5 μL of diluted a capture antibody per well using        plate coating buffer (with Triton).    -   4. Apply 5 μL of diluted capture antibody directly to the center        of the working electrode surface being careful not to breach the        dielectric. The droplet should spread over time to the edge of        the dielectric barrier but not cross it.    -   5. Allow plates to sit uncovered and undisturbed overnight.

The vesicle containing sample and a solution containing the labeleddetection antibody are added to the plate wells. The detection antibodyis an anti-target antibody labeled with an electrochemiluminescentcompound, MSD SULFO-TAG label. Vesicles present in the sample bind thecapture antibody immobilized on the electrode and the labeled detectionantibody binds the target on the vesicle, completing the sandwich. MSDread buffer is added to provide the necessary environment forelectrochemiluminescence detection. The plate is inserted into a readerwherein a voltage is applied to the plate electrodes, which causes thelabel bound to the electrode surface to emit light. The reader detectsthe intensity of the emitted light to provide a quantitative measure ofthe amount of vesicles in the sample.

Nanoparticles.

Multiple sets of gold nanoparticles are prepared with a separateantibody bound to each. The concentrated microvesicles are incubatedwith a single bead type for 4 hours at 37° C. on a glass slide. Ifsufficient quantities of the target are present, there is a colorimetricshift from red to purple. The assay is performed separately for eachtarget. Gold nanoparticles are available from Nanosphere, Inc. ofNorthbrook, Ill., USA.

Nanosight.

A diameter of one or more vesicles can be determined using opticalparticle detection. See U.S. Pat. No. 7,751,053, entitled “OpticalDetection and Analysis of Particles” and issued Jul. 6, 2010; and U.S.Pat. No. 7,399,600, entitled “Optical Detection and Analysis ofParticles” and issued Jul. 15, 2010. The particles can also be labeledand counted so that an amount of distinct vesicles or vesiclepopulations can be assessed in a sample.

Example 29 KRAS Sequencing in CRC Cell Lines and Patient Samples

KRAS RNA was isolated from vesicles derived from CRC cell lines andsequenced. RNA was converted to cDNA prior to sequencing. Sequencing wasperformed on the cell lines listed in Table 18:

TABLE 18 CRC cell lines and KRAS sequence DNA or KRAS Genotype KRASGenotype Cell Line Vesicle cDNA Exon 2 Exon 3 Colo 205 Vesicle cDNA Wildtype (WT) WT Colo 205 DNA WT WT HCT 116 Vesicle cDNA c.13G > GA WT HCT116 DNA c.13G > GA WT HT29 Vesicle cDNA WT WT Lovo Vesicle cDNA c.13G >GA WT Lovo DNA c.13G > GA WT RKO Vesicle cDNA WT WT SW 620 Vesicle cDNAc.12G > T WT

Table 18 and FIG. 14 show that the mutations detected in the genomic DNAfrom the cell lines was also detected in RNA contained within vesiclesderived from the cell lines. FIG. 14 shows the sequence in HCT 116 cellsof cDNA derived from vesicle mRNA in (FIG. 14A) and genomic DNA (FIG.14B).

Twelve CRC patient samples were sequenced for KRAS. As shown in Table19, all were wild type (WT). All patient samples received a DNasetreatment during RNA Extraction. RNA was extracted from isolatedvesicles. All 12 patients amplified for GAPDH demonstrating RNA waspresent in their vesicles.

TABLE 19 CRC patient samples and KRAS sequence Sample KRAS Genotype KRASGenotype Sample Type Stage Exon 2 Exon 3 61473a6 Colon Ca 1 WT WT62454a4 Colon Ca 1 WT WT 110681a4 Colon Ca 1 WT Failed sequencing28836a7 Colon Ca 1 WT Failed sequencing 62025a2 Colon Ca 2a WT WT62015a4 Colon Ca 2a WT WT 110638a3 Colon Ca 2a WT WT 110775a3 Colon Ca2a WT WT 35512a5 Colon Ca 3 WT WT 73231a1 Colon Ca 2a WT WT 85823a3Colon Ca 3b WT WT 23440a7 Colon Ca 3c WT WT 145151A2/3 Normal WT WT139231A3 Normal WT Failed sequencing 145155A4 Normal WT Failedsequencing 145154A4 Normal WT Failed sequencing

In a patient sample wherein the patient was found positive for the KRAS13G>A mutation, the KRAS mutation from the tumor of CRC patient samplescould also be identified in plasma-derived vesicles from the samepatient. FIG. 14 shows the sequence in this patient of cDNA derived fromvesicle mRNA in plasma (FIG. 14C) and also genomic DNA derived from afresh frozen paraffin embedded (FFPE) tumor sample (FIG. 14D).

Example 30 Immunoprecipitation of Protein—Nucleic Acid Complexes

This Example examined the levels of miRNAs in plasma contained incomplexes with Ago2, Apolipoprotein AI, and GW182. Specifically, miRNAlevels were assessed after co-immunoprecipitation with antibodies toAgo2, Apolipoprotein AI, and GW182.

To carry out the immunoprecipitation, human plasma was incubated withantibodies bound to protein G beads against Ago2, Apolipoprotein AI,GW182, and an IgG control. To prepare the beads, 10 μg of anti-AGO2(ab57113, lot GR29117-1, Abcam, Cambridge, Mass.), anti-ApoAI(PA1-22558, Thermo Scientific, Waltham, Mass.), anti-GW182 (A302-330A,Bethyl Labs, Montgomery, Tex.) or anti-IgG (sc-2025, Santa Cruz, SantaCruz, Calif.) were conjugated to Magnabind protein G beads (Cat. #21349,Thermo Scientific) or Dynabead Protein G (Cat. #100.04D, Invitrogen,Carlsbad, Calif.). 200 μl of beads were placed in a 1.5 ml eppendorftube and placed on a magnetic separator (Cat. #S1509S, New EnglandBiolabs, Ipswich, Mass.) for one minute. The storage buffer was removedand discarded. The beads were washed once with 200 ml of phosphatebuffered saline (PBS). The antibodies were allowed to bind the beads in200 μl PBS for 30 minutes at room temperature (RT) and then for anadditional 90 minutes at 4° C. The antibody-bound beads were placed onthe magnetic separator for one minute. Unbound antibody was removed anddiscarded. The beads were washed three times with ice cold PBS.

The antibody conjugated beads were resuspended in 200 μl of PBS andmixed with 200 μl of human plasma from normal subjects (i.e., withoutcancer). The mixture was allowed to roll overnight on a ThermoScientific Labquake Shaker/Rotisserie at 4° C. Following the overnightincubation, the beads were placed on the magnetic separator for 1 minuteor until the solution turned clear. The beads were washed three timeswith 200 μl cold PBS and once with 200 μl of an NP-40 wash buffer (1%NP-40, 50 mM Tris-HCl, pH 7.4, 150 mM NaCl and 2 mM EDTA). Following theNP-40 buffer wash, the samples were rinsed one additional time with 200μl of cold PBS. The beads were placed on the magnetic separator for oneminute. The beads were the brought back to the original starting volumein 200 μl of PBS. Three quarters of the sample was used for RNAisolation as described previously (Arroyo et al., 2011). The remainingwas stored at −20° C. for Western analysis.

The isolated RNA was screened for miR-16 and miR-92a using ABI Taqmandetection kits ABI_(—)391 and ABI_(—)431, respectively (AppliedBiosystems, Carlsbad, Calif.). RNA was quantified against syntheticstandards. The supernatant was collected and analyzed for selectedmiRNAs (miR-16 and miR-92a). The levels of miR-16 and miR-92a detectedare shown in FIG. 15. As shown in the FIG. 15A and FIG. 15B,respectively, miR-16 and miR-92a co-immunoprecipitated with Ago2 andGW182 using Magnabeads at much higher levels than the IgG control(compare bars denoted as “Beads”). Co-immunoprecipitation with Dynabeadswas unsuccessful for technical reasons which were not explored further.

Potential source(s) of miRNA from human plasma include vesicles and/orcirculating Ago2-bound ribonucleoprotein complexes (RNP). miRs can besimultaneously isolated from complexes with AGO1-4 and vesicles usingcapture of GW182. This Example shows that miR-16 and miR-92aco-immunoprecipitate with AGO2 and GW182 in human plasma.

Example 31 Flow Sorting of microRNA Complexes

Circulating microRNA derived from specific tissues can be isolated usingtissue specific biomarkers to isolate the microvesicles and othermicroRNA complexes. This Example shows that microRNA in a PCSA/Ago2double positive sub-population in human plasma can distinguish prostatecancer from non-cancer.

Plasma samples from three subjects with prostate cancer and three malesubjects without prostate cancer were treated to concentrate vesicles asin Example 17. The concentrated vesicles were stained using optimizedconcentrations of antibodies against PCSA, a prostate specificbiomarker, and Ago2 (ab57113, lot GR29117-1, Abcam, Cambridge, Mass.).The antibodies used were anti-PCSA labeled with PE and anti-Ago2 labeledwith FITC. Positive gates were set using matching isotype controlantibodies to define positive and negative regions. Sorted populationswere selected based on regions as shown in FIG. 16. The Beckman CoulterMoFlo-XDP cell sorter and flow cytometer was used to isolated positiveevents using the high-purity sorting mode (i.e., “Purify 1/Drop”) toensure that sorted events were pure to >90%. The MoFlo-XDP is capable ofsorting two populations at rates of up to 50,000 events per second. Toensure purity and efficiency of the particle sort, the rate was between200-300 events per second on average. Positive events were sorted intothree 2 ml tubes and reserved for subsequent miR analysis.

Once sorted, the microRNA content from each prostate specificsubpopulation was evaluated. When a comparison of total concentratedplasma-derived microvesicles was made, little differential expression ofmiR-22 was observed between prostate cancer (PrC) and non-cancer samples(i.e., normals) (FIG. 17A). Similar results were observed with mean copynumber levels of miR-22 from total RNA isolated from each PCSA/Ago2double population (FIG. 17B). Without taking microRNA levels intoaccount, the number of PCSA/Ago2 double positive events from each plasmasample did not significantly distinguish cancer from non-cancer (FIG.17C). However, a clear separation was observed between prostate cancerand non-cancer when the number of observed copies of miR-22 from eachsort was divided by the specific number of events from each sort (FIG.17D). In this latter case, higher levels of miR-22 per PCSA/Ago2 doublepositive complexes were observed in all PCa plasma samples as comparedto normal.

Example 32 Protocol for Immunoprecipitation Purification of CirculatingMicrovesicles

This Example provides a protocol for immunoprecipitation of circulatingmicrovesicles (cMVs) from using antibodies to two markers. Anyappropriate antibody can be used that will capture the desired vesiclemarkers of interest. The protocol can further be applied to differentsample sources, such as analysis of vesicles from various bodily fluids.In this Example, prostate specific vesicles are doubleimmunoprecipitated from plasma using antibodies to PCSA and CD9.

-   -   1) Thaw 1 ml plasma from a subject of interest. For example, a        subject having prostate cancer or a control, such as a normal        male without prostate cancer.    -   2) Stain the unconcentrated plasma with 40 μl anti-PCSA-PE        conjugated antibody and 45 μl of anti-CD9-FITC to the plasma.    -   3) Mix and incubate for 30 minutes in the dark at room        temperature.    -   4) Concentrate the plasma using 300 kD columns from 1 ml to 300        μl to remove unbound antibodies.    -   5) Remove and set aside 50 μl of concentrated plasma to        determine the starting content. Save for flow analysis, store 4°        C.    -   6) Add 20 μl of anti-FITC microbeads to the remaining 250 μl of        stained concentrate.    -   7) Incubate in the dark, refrigerated on a shaker for 30 mins.    -   8) Prepare MultiSort columns (Miltenyi Biotec Inc., Auburn,        Calif.) by washing the columns with 3×100 μl washes with        Separation Buffer (Miltenyi) off the magnet.    -   9) After the 30 minute incubation with anti-FITC microbeads        (Miltenyi), dilute the stained and labeled plasma by adding 200        μl buffer to reduce viscosity. Dilute further if still too        thick.    -   10) Add the ˜470 μl plasma solution to the top of a first washed        column, column 1, sitting on the magnet.    -   11) Allow the plasma solution to flow through.    -   12) Add 2×100 μl washes to the upper reservoir to remove        un-magnetized particles.    -   13) Total flow through for column 1 is ˜670 Save for        phenotyping.    -   14) Remove column 1 from the magnet.    -   15) Add 300 μl of buffer and plunge firmly to remove magnetized        cMVs from column 1.    -   16) Add 10 μl Multisort Release Reagent (Miltenyi) to the        retained volume (300 μl).    -   17) Mix and incubate 10 mins in the dark at 4° C.    -   18) An optional wash step can be performed to remove released        microbeads as necessary.    -   19) Add 20 μl MultiSort Stop Reagent (Miltenyi) to the cMV        solution.    -   20) Add 20 μl anti-PE MultiSort Beads (Miltenyi).    -   21) Mix and incubate 30 mins in the dark at 4° C.    -   22) Add the solution to the top of a second column, column 2,        while on the magnet.    -   23) Allow to flow through and collect as flow through.    -   24) Add additional 100 μl to wash any un-magnetized particles        off column 2 (˜450 μl).    -   25) Collect flow through and reserve for flow evaluation.    -   26) Remove column 2 from the magnet and add 300 μl buffer.    -   27) Plunge firmly to dislodge retained cells, reserve for flow        evaluation.    -   28) Add 10 μl of Release Reagent to cleave the beads.    -   29) Incubate 10 mins in the dark at 4° C.    -   30) Add 20 μl Stop Reagent.    -   31) Move to flow evaluation.

Vesicles can also be immunoprecipitated in a sample using a singleantibody and column step as desired. For example, prostate specificvesicles can be captured performing a single immunoprecipitation withanti-PSCA antibodies.

Flow Analysis.

Five populations collected above are analyzed by flow cytometry: 1)initial unseparated plasma; 2) flow through column 1; 3) retained column1; 4) flow through column 2; and 5) retained column 2. All populationshad CD9-FITC and anti-PCSA-PE added above. Beads were removed but thePE-conjugated antibodies remained on the cMVs and could be evaluated inthe flow cytometer.

-   -   1) Transfer solutions of cMVs to TruCount tubes for        quantification of cMVs/events.    -   2) Evaluate by flow cytometry using a Beckman Coulter MoFlo-XDP        cell sorter. Calculate the number of events based on TruCount        tubes (Beckman Coulter).

Example 33 Normalization of miRNA Expression in Plasma cMVs to cMV Level

This Example illustrates a method of normalizing miRNA expression in abodily fluid by combining fluorescence intensity of cell-type specificcMV surface protein markers, immunoprecipitation and nucleic aciddetection. This procedure allows for the amplification of a biomarkersignal between groups of interest. This Example illustrates thisapproach to distinguish plasma samples from subjects with prostatecancer and normals (i.e., non-prostate cancer) using miR-22, a microRNAwhich has been shown to be up-regulated in prostate cancer. See Zhang etal. microRNA-22, downregulated in hepatocellular carcinoma andcorrelated with prognosis, suppresses cell proliferation andtumourigenicity. Br J Cancer 103:1215-20 (2010).

Plasma microvesicles from prostate cancer and normal donors were doublyimmunoprecipitated with an anti-CD9 antibody (CD9-FITC BD BiosciencesCatalog #555371, BD Pharmingen, San Diego, Calif.) and an anti-PCSAantibody (prepared in-house) using the approach outlined in Example 32.FIG. 18A shows the input plasma for an exemplary sample using a BeckmanCoulter MoFlo-XDP cell sorter and flow cytometer to identify positiveevents. In FIG. 18A, it can be seen that whole plasma has mostly doublenegative events (i.e., CD9−/PCSA−). There are some double positives(i.e., CD9+/PCSA+) in the top right quadrant denoted as R7. Followingthe double immunoprecipitation comprising capture on a first CD9 columnfollowed by release and a second capture to a second PCSA column, theobserved cMV population is significantly enriched in CD9+/PCSA+ doublepositive events. See FIG. 18B, which shows the population after thedouble immunoprecipitation.

The populations described above were lysed and evaluated for miRNA/mRNAcontent. The levels of miR-22 in unprocessed plasma were higher innormal than cancer samples. See FIG. 19A. A similar trend was observedwith miR-22 levels from total RNA isolated from total cMVs inconcentrated plasma. See FIG. 19B. However, the raw copy number ofmiR-22 in isolated CD9+/PCSA+cMVs was higher in the cancer samplescompared to non-cancer. See FIG. 19C. This separation was enhanced whencomparing the number of observed copies of miR-22 from each doublepositive cMV population to the matched PCSA MFI obtained as in Example20 using anti-PCSA as a capture agent. See FIG. 19D.

In a second experiment, a single immunoprecipitation using anti-PCSAantibodies was performed using the above method and the resulting cMVpopulation was evaluated by flow cytometry. The results of flow analysisof an exemplary sample of input material are shown in FIG. 18C. Therewere few PCSA+ events at the outset. Following the immunoprecipitationwith anti-PCSA antibodies, the population was strongly enriched forPCSA+cMVs. See FIG. 18D. This population was then lysed and evaluatedfor miRNA/mRNA content from both prostate cancer donor plasma and normaldonor plasma. See FIGS. 19E-19G. As with the double immunoprecipitation,the separation between cancer and normal was enhanced when comparing thenumber of observed copies of miR-22 from each PCSA positive cMVpopulation to the matched PCSA MFI.

Example 34 Score for Normalization of Antibody Captured miR Expressionto Antibody Level

This Example illustrates a method of producing a score to distinguishplasma from cancer patients from non-cancer patients by detecting alevel of miRNAs inside circulating microvesicles (cMVs).

Plasma from prostate cancer patients and normal individuals (i.e.,without prostate cancer) was filtered with a 1.2 uM filter thenconcentrated with a 150 kDa column to concentrate cMVs. See Example 17.In order to measure prostate specific cMVs, a PE conjugated anti-PCSAantibody was incubated with 200 μl of the concentrate. The PCSA labeledconcentrate was purified for PCSA expressing cMV by using a Miltenyimagnetic column. See Example 32. RNA from the retained beads containingthe PCSA expressing cMV was isolated using Qiagen miRNeasy (Qiagen Inc.,Valencia, Calif.). 60 μl of the PCSA labeled concentrate was run on amicrosphere assay consisting of HPLC purified antibodies to PCSA, PSMA,B7H3, CD81, CD63 and CD9. The antibodies to PCSA, PSMA and B7H3 wereused as capture agents and fluorescently labeled antibodies to CD81,CD63 and CD9 were used as detectors. See Examples 22-23. Medianfluorescence levels (MFI) were recorded.

RNA was isolated from each sample concentrate. The copy number of miR-22and let-7a was determined using Taqman assays with a pre-amp step on anABI 7900 (Applied Biosystems, life Technologies, Carlsbad, Calif.). Tocalculate a diagnostic score, the copy numbers of miR-22 and let-7a ineach sample were multiplied by 10 and then divided by the MFI of PCSA inthat sample as determined using the microsphere assay. The sum of thesevalues was added to the MFI value of PSMA from the microsphere assay.The average of all three values produces a diagnostic score which wasused to differentiate between cancers and normals. In other words, thediagnostic score equals the average of 10*miR22/PCSA MFI, 10*let-7a/PCSAMFI and PSMA MFI.

A threshold for the score was determined using 40 randomly selectedsamples. Using a threshold score of 531 or above to distinguish cancer,a performance of 83% sensitivity and 63% specificity was obtained. SeeFIGS. 20A and 20B, wherein the threshold is indicated by the dashedhorizontal line. FIG. 20C shows an ROC curve generated with the data.The AUC was 0.77. This threshold was used to classify an independentcohort of 20 samples, resulting in a performance of 82% sensitivity and67% specificity.

Example 35 miRNA Signatures of PCa

This Example illustrates miRNA signatures of circulating microvesicles(cMVs) that can be used to distinguish prostate cancer.

Twenty-one of the samples described in Example 34 that were purified forPCSA expressing cMVs were used to identify microRNA that distinguish thevarious sample populations. The sample chort comprised eight prostatecancers, three high grade PINS, two inflammatory disease, and sixnormals (i.e., no prostate conditions). The miR content of the isolatedRNA from the PCSA expressing cMVs were analyzed using Exiqon cards asdescribed in Example 25. Statistical analysis was performed to identifymiRs that significantly differentiate cancer samples. The top 17 miRsincluded miR-182, miR-663, miR-155, mirR-125a-5p, miR-548a-5p,miR-628-5p, miR-517*, miR-450a, miR-920, hsa-miR-619, miR-1913,miR-224*, miR-502-5p, miR-888, miR-376a, miR-542-5p, miR-30b* andmiR-1179. FIG. 21 shows illustrative plots for miR-920 (FIG. 21A) andmiR-450a (FIG. 21B). As shown in the figure, miR-920 is overexpressed inconfounding diseases whereas miR-450a is down regulated in cancers.

Example 36 Analysis of Protein, mRNA and microRNA Biomarkers inCirculating Microvesicles (cMVs)

Vesicles protein biomarkers are analyzed using a microsphere-basedsystem. Selected antibodies to the target proteins of interest areconjugated to differentially addressable microspheres. See, e.g.,methodology in Example 22. After conjugation, the antibody coatedmicrospheres are washed, blocked by incubation in Starting BlockBlocking Buffer in PBS (Catalog #37538, Thermo Scientific, a division ofThermo Fisher Scientific, Waltham, Mass.), washed in PBS and incubatedwith the concentrated cMVs from plasma as described below. Followingcapture of cMVs, the microsphere-cMV complexes are washed and incubatedwith phycoerythrin (PE) labeled detector antibodies to the tetraspaninsCD9, CD63 and CD81 (i.e., PE labeled anti-CD9, PE labeled anti-CD63, andPE labeled anti-CD81) and washed prior to being detected on themicrosphere reader. The fluorescent signal from 100 microspheres ismeasured and the median fluorescent intensity (MFI) for eachdifferentially addressable microsphere—each corresponding to a differentcapture antibody—is calculated. Various combinations of detector andcapture antibodies are examined in addition to the tetraspanin detectorsdescribed above.

Flow cytometry is used to determine the total number of cMVs in thepatient samples. Patient plasma samples are diluted 100 times in PBSthen incubated for 15 min at room temperature (RT) in BD Trucount tubes(BD Biosciences, San Jose, Calif.) for quantification of events persample. Trucount tubes contain a known number of fluorescent beads thatcan be used to normalize events for each sample by flow cytometry.Sample acquisition by FACS Canto II cytometer (BD Biosciences) andanalysis by FlowJo software (Tree Star, Inc., Ashland, Oreg.) are usedto determine the number of sample events and number of Trucount beadsper tube. Calculation of absolute number per sample is obtainedfollowing manufacturer's instructions (BD Biosciences) and adjustment bydilution factor as necessary.

MiRNAs are examined from the payload with cMVs from the plasma samples.cMVs are concentrated and the miRNAs are extracted using a modifiedTrizol method. Briefly, cMVs are treated with Rnase A (20 μg/ml for 20min @ 37° C.; Epicentre®, an Illumina® company, Madison, Wis.) followedby Trizol treatment (750 μl of Trizol LS to each 100 μl) and vortexedfor 30 min at 1400 rpm at room temperature. After centrifugation, thesupernatant is collected and RNA is further purified with the miRNeasy96 purification kit (Qiagen, Inc., Valencia, Calif.) and stored at −80°C. Forty ng of RNA are reverse transcribed and run on the Exiqon qRT-PCRHuman panel I and II on an ABI 7900 (Applied Biosystems, lifeTechnologies, Carlsbad, Calif.). See, e.g., Examples 13-14, 25. C_(T)values are calculated using SDS 2.4 software (Applied Biosystems). Allsamples are normalized to inter plate calibrator and RT-PCR control.

Messenger RNA (mRNA) is also examined in the cMV payload from the plasmasamples. cMVs are isolated and treated with RNase A as above. mRNA isextracted using a modified Trizol method as above and purified with aQiagen RNeasy mini kit precipitating with 70% ethanol (Qiagen, Inc.).The collected RNA is reverse transcribed and Cy-3 labeled usingAgilent's “Low Input Quick Amp Labeling” kit for one-color geneexpression analysis according to the manufacturer's instructions(Agilent Technologies, Santa Clara, Calif.). Labeled samples arehybridized to Agilent's Whole Genome 44K v2 arrays and washed accordingto manufacturer's specifications (Agilent Technologies). Arrays arescanned on an Agilent B scanner (Agilent Technologies) and data isextracted with Feature Extractor (Agilent Technologies) software.Extracted data is normalized with a global normalization method andanalyzed with GeneSpring GX software (Agilent Technologies).

Both miRNA and messenger RNA can be examined from specificsubpopulations of cMVs from the plasma. For example, cMVs areconcentrated then the population that is positive for PCSA is isolatedusing immunoprecipitation. See Examples 32-33. The PCSA+cMVs areisolated and miRNA and mRNA is isolated and analyzed as described above.The same methodology is used to examine the miRNA and mRNA content ofvesicles isolated using different capture agents directed to differentvesicle surface antigens of interest. In addition, the vesicles can beisolated that are positive for more than one surface antigen. SeeExamples 32-33.

Normalized analyte values are imported into either R (available from TheR Project for Statistical Computing at www.r-project.org) or SASsoftware (SAS Institute Inc., Cary, N.C.). The data is filtered usingappropriate quality control measures and transformed prior to analysis.Analysis is performed as follows:

Signature Performance Evaluation (for Pre-Specified or Novel Signatures)

The sample sets generated using the methods above (i.e., payloadanalysis of isolated vesicle populations) can be used to evaluate theperformance of a bio signature that is fully specified prior to eitherthe unblinding of clinical outcome or to the unblinding of clinicallaboratory testing of samples. In such a case, the signature isconsidered pre-specified and must be applied, unmodified, to new analytedata on this sample set to obtain predicted outcomes for all samples.Performance of the pre-specified signature is evaluated by comparingpredicted and true outcome (for example, in terms of diagnosticsensitivity, specificity, and accuracy). Statistics include performanceestimates and confidence intervals.

For signatures that are not pre-specified (i.e. that are derived withforeknowledge of both clinical outcome and laboratory testing results ofsamples), these samples may still be used to evaluate the performance ofthe signature. However, to reduce potentially biased estimates ofperformance, statistical analyses are performed nested within a k-foldcross validation loop that includes marker selection and classprediction steps as described below.

Marker Selection for Novel Signatures

Markers are included in novel signatures if they are statisticallyinformative by testing for their association with disease outcome usinga subset of commonly applied techniques known to those of skill in theart. These include: 1) Welch test—robust parametric statistical test fordifference between group means when variances are unequal; 2) Wilcoxonsigned-rank test—robust non-parametric statistical test that can beinterpreted as showing an improvement in ROC AUC (above 0.50); 3)Youden's J—calculated as the maximum combined sensitivity andspecificity for a marker, across all possible diagnostic thresholds.Statistical significance is evaluated via permutation tests.

Markers are judged statistically informative if the test is significantin the context of the number statistical tests performed. Morespecifically, comparison-wise p-values are adjusted for multipletesting—e.g. using false discovery rate thresholds or by control offamily-wise error rates.

Formation of Novel Signatures

Once a subset of informative markers is identified in the markerselection stage described above, novel multi-marker models are formedusing well-established modeling techniques. Parameters for signaturesare estimated by training the models on the full training data set, andperformance for the signature is evaluated as described under “Signatureperformance evaluation” using the approach “for signatures that are notprespecified.” Simple and well-established modeling techniques are usedin these steps, including: discriminant analysis, support vectormachines, logistic regression, and decision trees. Results for allmodels will be reported and optimal markers panels are identifiedaccordingly.

Additional a posteriori analyses are performed on the data set forclinical variables of interest as available. Such variables include age,ethnicity, PSA levels, digital rectal exam (DRE) results, number ofprevious biopsies, indication for biopsy and biopsy result (e.g. HGPIN,ATYPIA, BPH, prostatitis or prostate cancer), and the like. Suchanalyses are performed by introducing covariates or stratificationvariables into previously defined models. P-values are corrected formultiple testing.

Example 37 Biological Pathway Expression in Circulating Microvesicles(cMVs)

In this Example, expression profiling of mRNA payload in cMVs isperformed. Pathway analysis of mRNAs expressed in the cMVs is performedto identify the most significant biological pathways.

To profile mRNAs in whole vesicle populations, cMVs were isolated from 1ml of plasma from three prostate cancer and three non-cancer controlsamples using filtration and concentration as described in Example 6.RNA was extracted from 100 μl of plasma concentrate, which was thensubdivided into 25 μl aliquots for lysis with Trizol LS (Invitrogen, bylife technologies, Carlsbad, Calif.) after treatment with RNASE A. Theaqueous phase from each of the four aliquots was precipitated with 70%ethanol, combined on a single Qiagen mini RNA extraction column (Qiagen,Inc., Valencia, Calif.), and eluted in a 30 μl volume. The eluted RNAcan be difficult to reliably quantify by standard means. Thus, a 10 μlvolume was used for the subsequent labeling reactions. Samples were cy-3labeled with “Low Input Quick Amp Labeling” kit from Agilent forone-color gene expression analysis according to the manufacturer'sinstructions (Agilent Technologies, Santa Clara, Calif.), with thefollowing modifications: 1) The spike-in mix for Cy3 labeling wasaltered so that the third dilution was 1:5 and 1 μl was added to eachsample; 2) 10 μl of sample was reduced in volume to 2.5 μl using avacufuge in duplicate for each sample; 3) Every sample was processed induplicate throughout the protocol until the purification step of theamplified samples. At the beginning of the purification protocol, theduplicate samples were combined and subsequently passed through thecolumn; 4) The samples were not quantified after purification but ratherthe full volume of the purified sample was hybridized to the array.Labeled samples were then hybridized to Agilent Whole Genome 44Kmicroarrays according to manufacturer's instructions (AgilentTechnologies). Data was extracted with Feature Extractor software(Agilent Technologies) and analyzed with GeneSpring GX (AgilentTechnologies). 4291 mRNAs were found to be present in the concentrate,including those found in Table 20. The GeneSpring software was used toidentify pathways that correlated with the expression patterns.Following the above analysis, the androgen receptor (AR) and EGFR1pathways were the most significantly expressed pathways in the vesiclepopulation. The members of the AR and EGFR1 pathways are shown in Table21:

TABLE 20 mRNA Expression in Total cMVs DNAJA1, RPL23, RPS13, VASH1,YWHAZ, ORMDL3, UBE2I, DNTTIP2, RPL18, HLA-DRB1, C6orf62, GGA1, IMP3,JUN, NUDC, HLA-DRB5, NDUFB9, BTF3L1, RNF11, KLK3, DENND4B, NECAP2,PLAC8, C14orf166, HNRNPU, MTHFS, TCP1, U2AF1, MRPS12, IL8RBP, OAZ1,STRA13, C2orf79, EBNA1BP2, HMGN1, PYCR2, CREB3L1, CHRDL1, ZNF254, UBE2B,GAPDH, NDUFV2, LCP2, VDAC3, TSSC1, RBM22, YWHAZ, GABARAPL2, PPP1CA,FCN1, DNAJB6, CD44, KIAA0430, HSP90AA1, ATP5J2, C17orf72, GLCCI1, 7-Sep,CTSC, TNRC18, ARL6IP1, HLA-J, GPX4, SYK, RPL23AP53, SDPR, SFRS3, RPL35A,UBC, TALDO1, NKG7, MFN2, TINF2, SNCA, LYN, RHOC, PPIA, RHOA, TPM3,ATP6V1F, MYO1F, MUC5B, HS2ST1, BOLA3, HMGN1, FKBP1A, LOC100131582,DNAJA1, RPL10, SYCE1L, RPS25, RPS2, CDKN2A, AHSP, EPB42, C21orf7,LOC100288578, CFD, LOC100134569, LCK, CD52, HSD17B10, OAZ1, MAT2A, DCI,HSPA1A, RPL23A, CCT3, AQP2, LSP1, RNF10, RPL39, EIF3E, RPS29, MLXIPL,KPNA2, UTF1, TALDO1, CRLF3, YWHAB, HBQ1, SSR4, ST13, HLA-DRB3, PFN1,NOS3, FAM102B, WHAMM, PRR13, NPEPL1, MCL1, LOC100132247, NONO, IL26,CCDC69, LBH, RPL35, NCOR2, FBRS, RPS10, RPL4, FAM128B, RPS10, FBRSL1,DYNLRB1, ISCU, PLA2G16, PRR5, RNASEH2A, TNRC6B, RPL36, PGLS, LGALS9C,NCOA4, SFRS5, CPNE5, C3AR1, RPL14, EEF1D, EMX1, STK10, RPS10, ZFP36,C21orf58, SPATA2L, MTA1, FLJ43681, MRPS6, HIST1H2AD, PSMD8, ITGB2, RPSA,PMEPA1, PARP1, TRAPPC5, ARPC5L, MRPL41, PDE4C, CCDC108, ANKK1, APBB1IP,MCTS1, TCL1A, HLA-A, ZNF775, POLD4, ACTB, CYBA, DAD1, ARF1, MRPS21,FAM107A, RPL38, SMARCC2, DNAJB2, ANXA1, EVPL, PHPT1, ZNF784, GRB2,SCYL1, VPS4A, RPL23AP7, CTNNB1, HIST1H4H, SMARCC2, RPL36AL, WIPI2,VPS35, C10orf125, RPL10A, RPS15, CARD16, GPSM3, EIF3C, FPR1, ICT1, BZW1,C15orf28, HLA-A, RAB18, ETFB, IL1B, SLC45A4, BAX, IFI27, PPIA, NYX,SLC27A1, ANXA11, ACRBP, TERT, NDUFA6, ZCCHC18, CDC42, RPL30, TNRC4,PWP1, LOC729046, NDUFA4, UFC1, TUB, RDBP, ERBB2, OAZ1, RPS3, TPSG1,HNRNPA1L2, ARMCX6, FAM43B, C16orf11, CASP3, MIP, CUTA, PABPC1,LOC283663, HMOX1, RPS10P7, GNAS, C4orf3, MRPS21, SPARC, LSM3, TBCB,GRAMD1C, CHMP4A, RASL10B, LOC100293539, NDUFC1, CWC15, CHRNB2, KRT10,SNX3, RAP1A, CPLX2, ILDR1, HIST1H2Bi, ADAMTS13, MRPL34, FKBP3, ZNF680,SRRM3, MYPOP, FTH1, MMD, POLR2F, ODC1, BLOC1S1, UBE2L3, MCM7, C14orf156,RPSA, ARHGAP1, ATP5SL, SOD1, RANBP1, CARD8, NACA, NCRNA00152, SUMO2,H3F3C, SNRPF, YWHAQ, SCLT1, DAD1, SNTA1, DHRS1, CYB5R3, SNX5, SLC25A5P1,ZNF714, C9orf131, MTMR14, RNF44, LOC100132161, HLA-DPB1, OR10H2, ID2,SSRP1, RPS27, MXI1, TEAD3, LOC648771, TMEM158, TIAM1, RPSA, IFI27L1,HINT1, USP33, H2AFZ, BLOC1S2, TNFAIP8L2, HMGB1L1, C20orf108, RPS29,LMO2, HNRNPA1L2, LOC647121, RAC1, NPC2, SMR3A, HIST1H4B, FXYD5, LARS,RALGDS, NBPF3, THEM5, MAPKAPK3, RPL23, TMSB10, MMP28, C19orf56, HMBS,PSMA2, MTCH1, GNB2L1, COX6B1, UBB, TIMM9, CASP8, BRD7, LCE3E, RPL14,MT1G, LBH, RPL3, RPL13, FLOT2, SYMPK, PMPCB, HMGN2, EEF1D, ROD1, PTP4A2,PCBP1, CACNB3, FHIT, TMBIM6, LCE1D, HRASLS5, TEF, TPT1, RPS15, SNHG5,RPL9, MIER1, MYC, DNAJC4, C6orf25, RPL21, CABP7, CTXN1, STMN1, FAM96B,SELK, COX17, SNRPB, FLJ22184, EIF3B, C12orf65, U2AF1, RPL32, FYN, SP5,LOC100130107, CCDC56, NBPF20, MMADHC, PRDX5, SPINK7, BTN3A2, TMEM38A,ZNF2, DECR1, NDOR1, CDK3, HNRNPA1L2, SMAD2, HCN2, TOMM20, PFN1, SFRS18,B2M, SUB1, PKM2, COX6A2, NLGN2, MBD2, RILPL2, CASP1, NACA, CCL5, RPL37A,RPL22, DYNLL1, SAT1, LSM5, LOC441245, ZFAND6, EEF1G, MAP3K3, LSM1,PSMB6, HBG1, EPHX3, HDAC1, LCE5A, PSMC1, MCM3, BAX, MRPL13, TUBA3D,MTIF3, NCF1, RPS17, RPL10, CIRBP, PSMA6, AMICA1, HNRNPA3, RPS25,C19orf56, POLE4, MAP1LC3B, FASTK, RPL23AP82, UQCRC1, RPL24, PRELID1,RPS19, RPL5, PGK1, KIAA0494, HP1BP3, DMWD, RPL26, EIF6, PCBP2, TRMT112,SEC11A, RPL21, MEI1, CCNI, NCKAP5L, TMSL3, AHNAK, BTF3, HNRNPA1, PTPN6,SIPA1L1, POLR2J, C3orf1, C6orf48, LOC100128731, PCBP1, C17orf49, ETS2,HIST1H3D, TUBB6, SH3BGRL3, CIAO1, FAM58A, HIST1H2BE, MRPL20, RPL29,HIST3H2A, LOC407835, RPL37, RAB35, FLI1, TNFRSF14, FAM129A, GNG5, RPL24,JAK1, C5orf39, LILRB3, C16orf3, A2M, ZNF592, NPHS2, HIGD1A,RP3-377H14.5, KRTAP5-8, PIP5K1C, FAM124A, C22orf32, S100A13, IFITM1,CSDA, NDUFA6, RPL12, FTH1, RARRES3, ZFAND5, RPL29, DAP3, RNF7, COX4I1,FAM110A, FOXN3, CXCR4, BBC3, RPS8, CD79A, POTEE, APOL3, PPM1A, FECH,RPLP0, EIF3K, LOC100293090, GGCT, TMEM93, RPS7, RAP1GAP, RABEP1, CEBPB,LGALS3, RCOR2, VIM, IFITM5, C1orf144, EIF3L, CAPNS1, NBPF10, S100A12,E2F2, COX5B, ZNF24, CTBP2, RABAC1, C11orf83, ANKDD1A, CD48, HSPB1, VAV1,LSM4, GLTPD1, SH3KBP1, RPL3, RPS2, RPS3A, LCE2A, DAB1, LDHA, CMTM3,MTPN, SCARF2, AES, CD4, LOC645955, PFDN2, ELP2, CTDSP2, LSM6, EIF2B1,METAP2, TRMT112, ARPC2, TCF4, APOL1, TRMT5, LOC647979, SLC39A4, RPS15A,EIF3L, WFDC3, EVX1, CHCHD2, ARHGAP25, SNW1, SNHG8, TBCA, KIAA0125,HIST1H4E, ACTB, KLF6, EEF1D, SLC2A1, ACADVL, RPS28, C19orf44, HDAC7,RPSAP52, NDUFA11, KIAA0240, CYTH1, GSTO1, MCAT, LAMP1, LOC644950,HIST1H3B, NDUFV1, MKRN1, TUBA4A, RPLP0, PALM, DNAJB5, PLEKHB2, UCRC,CLEC2D, CAMKK2, HMGN4, FAM119A, RPL18A, NGDN, RP11-431O22.2, KIF2A, HBB,SLC25A37, CMTM7, THOC7, ATP5G2, C7orf41, MAFA, VMA21, C14orf162, CLC,SLC25A5, LOC100132247, MKNK2, LOC729992, ELF1A1, SLC25A6, FAU, SCGB3A2,RGS2, BCL11A, MRPL18, CCDC50, NDUFS7, LOC729678, SYNPO, RPL23A, PRSS36,CALM1, TLE4, UBA52, MYL6, COMMD6, TCF7, ATP5F1, OTOF, HOXA3, CLPP,CACNA1C, CCDC86, BIRC5, SKP1, TSPO, RPS16, UBE2L3, GM2A, RPL36AP40,C9orf16, SLC9A3R2, STRBP, PPIAL4A, ADAMTS7, BRP44, ACP5, MPST, FBXO9,CCT4, CAND1, C10orf47, USP39, ST13, AKT2, NHP2, ENY2, SPG21, WIPF1,RAB37, TMEM37, TCEB1, BBX, RPSA, PDS5B, C20orf43, ZC3H6, ZNF493,LOC644563, 15-Sep, HIST1H1C, HECA, EXOSC9, MRPL55, RPS2P32, RPS27A,ANXA3, KCMF1, PLP2, KHDRBS1, RABGAP1L, OVCA2, SLC26A1, ATXN2L, C11orf9,RPL18A, MEX3D, TMEM14C, TSC22D1, HNRNPM, IGF2, NUCKS1, 5-Sep, NPEPPS,RPS20, BHLHE23, SQRDL, RPS4Y2, VNN2, RPS4P16, CORO1A, MIF, RPS26, RHEB,LOC642031, IGBP1, FOXA3, IGLL1, CCDC91, SF3A2, RPL14, HIST2H2BE,CCDC28A, SUMO2, H2AFZ, TRAF3IP3, VPREB3, MRPS34, HLA-DQA1, ZAP70, RHOH,TRABD, USMG5, 7-Sep, ZMAT2, NCAN, CXCL3, C19orf24, TK1, LOC100130107,TRIP12, RPL17, BANP, VPS18, ATF4, ZFAND5, KRAS, KCNK15, SEPHS2,LOC728449, HDAC7, RPS3A, NSUN5B, TOMM7, KHSRP, ALAS2, TRAF3IP3, GTF2A2,GRIN2D, RPL8, RBM8A, LOC100129250, NEDD8, GIGYF2, PSMD13, PABPN1, FAHD1,GABARAP, CTSA, HSPD1, KLHL34, IK, ITPA, GMFG, GNAZ, SEPW1, SCRT2,LOC100288165, TANK, TFPT, C16orf81, PDCL3, UBL5, DCAF5, RNH1, RYBP,GGT6, TNRC18, IMMT, PSMD7, NACAP1, UBE2K, NKX1-2, SQSTM1, GPBP1,SUPT4H1, C6orf106, ATP5I, RPLP0, EN2, METTL5, BZRAP1, IK, SHISA5,HNRNPA1L2, DNAJC15, PRKAR2A, SDK2, RAB8A, RPL34, INPP5D, PXN, AHCY,HNRNPA1L2, ZNF492, UQCRFS1, UBE2S, ATP5D, MRGPRF, NDUFA7, CSNK2B, CKS1B,S100P, MRPL34, PWP2, CD99, SERPINA1, HNRNPA1L2, BAG1, PCDHGA7, LY96,LZIC, POLD1, STUB1, AKIRIN2, POLR2L, CDC2L1, ZNF253, CCDC97, AIP, RAC2,DEAF1, SOX17, NPM1, RPS2, NEDD8, MRPL32, VPS24, NDUFS1, COX5A, SPRR1A,LOC649294, TRIM4, FRG1, EIF1, MAN1B1, DUT, ATP6V0C, EFHD2, C1orf175,PLEKHO1, HCLS1, ST13, MRPS25, LSMD1, NFE2L1, MRP63, C11orf10, MT3,G3BP1, UBC, HNRNPA3, LEPROT, PPP1R9B, STMN3, GTF2I, HIST1H1D, YWHAQ,HIST2H2AC, RPL37A, FRG1, MED13L, PPIAL4A, FBXO24, CAP1, RPL35, MGRN1,USP7, PTRF, KRTAP1-3, TMEM59, NDUFA13, MRPS24, UBA52, LOC440461, S100A6,CDC42, KIAA1462, SOD2, LSM14A, SAT1, C1orf151, RABGAP1L, SPIB, SAPS1,FAM129B, LIPE, PSMB8, MED10, SERBP1, NME2, GOLGA7, FLJ23867, KLF14,GLRX5, MRPL15, KCNK7, RPS11, PIM3, GMPR2, HCN4, RNASEH2C, CHMP2A, CSTA,ZNF713, BTG2, POTEF, CDC37, ZNF826, HNRNPC, YPEL5, RPS14, FTL, FOXD3,MXD1, RPL35, ATF6B, WWC3, DYNC1LI2, BAD, CRIP1, NEDD8, ZNF467, MRPS6,RABGAP1L, TPR, CCDC66, KISS1R, SEC14L1, BBS5, NP, YOD1, CGB1, S100A10,LOC100131262, PPBP, SDCBP, WASH1, C19orf28, RPS19BP1, PTMA, HBM,SERPINB1, RPS10, MYH14, C11orf73, C17orf88, CFL1, RPL23A, DNAJA1, IFI16,VAMP5, TUBA1C, MOGS, VDAC3, WDR1, GIMAP6, HSPA8, TP53TG3, UIMC1, PAPOLA,ZBTB45, RGS10, STRN4, EXOSC1, BCAM, ZNF444, MRPL53, MESDC1, C6orf115,DEXI, LOC126170, EID1, SELENBP1, EEF1D, RAB14, PDZK1IP1, TMEM201,FAM195B, PABPC1, C5orf4, OGDH, PPP1CA, HSP90AA1, C4orf14, CRTC2, TXNL1,C14orf43, RPL34, MNDA, NDUFV3, DRAP1, ANXA5, ARHGEF18, ARF5, SPSB3,tcag7.1015, LOC730144, RPL27A, ZNHIT1, HGS, TALDO1, CNN2, THRA, MRPS18C,FOXQ1, COMMD8, CTSG, BTF3, ARL6IP4, TUBA1A, C15orf21, LENG8, tcag7.873,MRFAP1L1, LGR4, FAM128B, IRX5, USP4, ZBTB8OS, AIF1L, CTSA, NDUFA12,CDKN1A, CAST, PPIA, EPB41, TMEM50A, RAN, EMP3, C13orf15, HNRNPD, MRPS36,TBC1D10B, INTS10, LOC541471, ANAPC5, RNF5, C9orf167, DUSP23, HNRNPA3,RTN3, TALDO1, TXN, FARSB, BIN2, PPIAL4A, OR2H1, LOC541472, ZC3H11A,EHBP1L1, RPS3A, RNF220, LOC389641, SEC11A, POU3F3, NRN1, MAGEE1, CYP2W1,C11orf48, HEMGN, HBXIP, SHARPIN, TMEM164, DOCK8, DVL1, HNRNPH1, MT1X,HNRNPC, AFTPH, VEGFB, GNG7, ZFPM1, ARHGAP27, HIST1H2BO, RRAS, C1orf56,LOC651250, RPS3A, EIF3M, LOC100132161, ZNHIT3, PTMA, C18orf10, NDUFB7,DEDD2, H2AFV, EIF4E2, RNF181, EIF3D, PIGY, ABR, LOC643997, SUMO2,ZFP36L1, TAGLN2, STAT6, NDUFV3, RAB11A, GNB1, EVI2A, C9orf163, LMOD1,BNIP3L, DENND2D, ATG3, AP2S1, BLMH, CASP4, GZMB, NGFRAP1, RPS17, AGAP3,NCL, ANXA2P1, RPS5, NDUFB2, PCMTD1, GCA, EIF1, FGFR1OP2, C19orf73,PSMB10, LOC439949, ROMO1, RGL4, CD86, YWHAZ, RSL1D1, RPS10, ATP5B,NCOA4, NFE2, APOA1BP, ARL6IP4, ATP5L, LOC100288418, C17orf61, MDFI,EEF1B2, A2ML1, ANK1, PUF60, HIST2H4B, DLX1, HAR1A, SOD1, KRT81, RPL12,NUP50, IGLL1, MT2A, CCDC12, ACTR2, LOC100130331, REPIN1, OXNAD1, SLC7A7,RNF151, C19orf43, C9orf78, DDX19A, NDUFB1, TNFAIP1, DPYSL2, VSIG10L,NDUFA1, RPS26, GTPBP6, KPNB1, TBCD, JMJD8, CYTIP, HIST1H2BJ, LOC283177,LTA4H, PPP1R14B, DIRC1, APTX, FBXO7, MT1B, TRIM10, SUMO2, HLA-B, UFD1L,PIP4K2A, SH3BP5, GH1, HRASLS5, CCL14, EIF4EBP1, MUC4, TACR2, USP17,HMGN2, SILV, TNXB, COX16, LOC100288755, ARL8A, ZNF429, SPEF1, RPS19,ALPP, AES, HIST3H2BB, PLEKHG6, CDKN2D, SYNPO, BAT3, ASCL2, MNT, PAQR6,H2AFZ, RPS10, PTPRE, UQCRQ, RBM3, hCG_19809, LHPP, RPL13A, AK2, ZFR2,RNF168, RPL21, SHMT2, POLR1D, MAP3K7IP2, MAX, CYP11B1, CAMKK2, HNRNPC,GIMAP7, PDZD7, DCAF10, LAGE3, FTL, PTPN4, HNRNPK, DEFA3, RNF167, PSMA4,CCT7, EIF3M, IQSEC2, FBXO25, ICAM2, ZMAT2, SUMO2, SNRPD1, GIPR, RIOK3,AIF1L, GNAS, RELB, LOC493754, PSORS1C2, MRPS18B, CASP4, CAPZA2, S100A4,TPM3, OGFR, RPLP0P3, CAPG, SLU7, H19, LOC100289641, MRP63, POLR2I,HMGB1, C22orf28, PTDSS1, RPL36A, PPIA, NDUFA1, DDB1, PSMA7, SUB1,ANP32B, PAFAH1B1, RBMS1, ATP6V0E1, TERF2IP, TUBA4A, TUBA1B, C12orf62,SKA2, BCL3, CDC42SE2, RPL23A, TPM4, KCNMB1, HIST2H2AA4, FBXL15, PTMS,LOC100289173, TESC, RRAGA, BLVRB, KRT3, HIST1H2AM, FTH1, CD3G, RPL29,TCTE3, PLCH2, RPL15, TMIGD2, SFRS7, SP100, LTB, GPT, NCF2, ADD1,LOC100294179, FOXO3, MED13L, BCKDHA, LOC100134663, HNRNPA1, SLC22A7,ZDHHC8, JOSD2, ARRDC2, ASB16, LOC100289587, PRPS1, SYNGR2, RPL9, GGT6,ZNF525, MRPL28, NIPBL, MS4A7, PKN2, ISCA2, PGLYRP1, ODF3L2, NDUFS4, SSB,CMIP, BAX, FAM107A, WDR45, NFE2L1, DDX1, SHISA4, MMP17, TMEM173, FGFBP2,GRIN1, HDGF, RNF114, CISH, TPT1, ABI3, CACYBP, HINT2, CKB, UBE2D3,LOC646577, IFITM3, ILK, LOC399851, TKT, UXT, NAB2, DYNLL1, SH3D20, SYF2,DARS, OAZ2, PHC2, WTAP, SOX3, COPS3, PREX1, EBP, RPL21, NDUFB11,ZC3H11A, GUK1, PP14571, BLVRA, SF3B2, MRPS2, RALBP1, PSMB1, NFKBIA,TNFSF12, RPS2P32, CAST, WHSC1L1, SLC40A1, TMEM160, MRPL20, CARS2, BASP1,SPSB4, CRELD2, APLN, PAK2, CD63, RAN, TUBA1C, CFL1, GSTP1, UBE2G2,HIST1H2AH, DEFA4, SERGEF, SARNP, RBM5, CBX1, ZNF716, DUSP9, ALAS2,AKAP13, SMEK1, PPP1R14B, BEX2, FCRLB, ECHDC2, MTA1, UQCRC2, MRPS33,TNFSF13B, HMGN3, RASSF1, RCC2, GRIPAP1, LOC119358, ICAM3, DRAP1, RPS27L,TMEM175, EIF4A3, NDUFB7, RPL21, SGTA, TOMM6, RPL21P44, C19orf60, LRP3,AMN, C19orf50, C13orf15, DCTN2, FAU, GSR, SAR1A, WDR1, HLA-DPA1,SLC25A37, TYROBP, EIF2AK1, UTP3, HSP90AA1, RPL22L1, MRPS15, POLR2G,UHMK1, PTEN, TCL6, SPCS1, AKR7L, RFXANK, H2AFJ, FAM65B, LCE1F, RPP21,PALM2-AKAP2, COX6C, RARS, RPL41, C6orf130, MFF, ATP6V0C, ALOX15B, MYL6,F8A1, RGS18, C11orf31, LOC100287593, MRPL14, CDCA3, FADD, ARHGDIB,HSP90B1, FLJ45445, H2AFY, HLA-DRB5, NPM1, GPI, ATP5E, GPR156, NAPRT1,TRADD, BCL2L12, LOC648771, PIGY, TNXB, HIST1H2AE, HMOX2, TARDBP, ACTB,RPS26, H2AFJ, SRRM1, NCF1, YWHAB, MAEA, TMSB4X, MT1H, LOC151009, RPL30,SPN, C20orf108, RPL23AP71, CSTB, HIST2H3D, BID, HIST2H3A, FAM26F, AGRP,RPL28, UBE2V1, ZNF219, FXYD5, VAMP2, EFHA1, MGC10814, RPL39, GZMH,GPR150, ADIPOR1, POLE3, PTMA, HSPA8, RPS3A, CEND1, CYFIP2, PIM1, 9- Mar,FAM104A, CYB561D1, PAPOLA, UBB, SPPL2B, CLDN5, RFNG, WASH1, EFTUD2,YWHAQ, GBP4, RPA2, IRX3, HLA-B, LOC644246, KDM5A, CASKIN1, TOMM5,MRPL51, TMSL3, ZNF746, MRFAP1, BLOC1S2, ARL4C, PRKCH, DOK1, CCDC85B,C10orf116, GTF2F1, RAB31, NTNG2, ZCCHC17, ADAMTSL5, MFSD1, DPEP3,LOC646960, RALBP1, SEC31A, HOPX, GNA13, SH3GLB1, STK24, PSPH, KLRB1,PDCD2, RNF5, ALPPL2, GRN, NPAS3, SLAIN2, ADRA2C, NPM1, NDUFS3,LOC284542, C14orf2, PPM1F, NKD2, CDH24, COX6A1, PRNP, PORCN, RBMX,EIF4A1, CCT6A, ATP5E, POLR2K, RPL7, CYP2B6, MFNG, C9orf25, GADD45B,PIGY, RNF10, PRR24, NAGK, FAM127B, PLEK, CCNDBP1, PNRC1, G3BP2,LOC440917, COTL1, HNRNPA1, RPL10A, MT1G, HIST1H2BH, IRF7, BCLAF1,hCG_2014417, STX10, CHCHD8, MRPL43, TMEM30B, AIP, CLIC1, RBBP7, GNAZ,BOLA3, RPL7A, ANAPC11, TRIM26, HERPUD1, LOC728875, TIMM10, YWHAQ, UBXN1,C6orf25, LOC648987, S100A9, NDUFB10, ZNF843, 9-Sep, EIF3A, TXNL4A, ACTB,CRTC1, GIMAP2, ALB, APPL1, MRFAP1, CAPN2, ZNF157, WNT10A, FXR1,LOC390282, MBP, LOC441455, HAGH, SF3B14, C17orf59, RPS23, HSPB1,LOC100133337, RHO, RTBDN, NAP1L1, NOSIP, SCRIB, MYO1C, TRAPPC5, PSMB4,TMEM111, C1orf229, LSM7, CDC42, GSTK1, ELF4, LOC100132247, KRTAP4-1,MOBKL1B, ZNF394, CSDE1, C18orf21, XRCC6, NDUFA2, CBL, POP7, NDUFB4,TUBB2C, RPS14, NPM1, CTTN, PEA15, EIF3G, MT1L, TNIP1, RPL34, TMEM191B,VWA1, MAPK1IP1L, C16orf13, UBE2V1, LOC100128942, CKLF, TRIM29, EEF1D,DPY30, HES4, UBA52, TGFBI, CXorf21, KIAA1310, HLA-C, C14orf119, SASH3,PXN, HIPK3, ATP6V0D1, LYAR, GBP3, HDAC4, FIS1, EXOC3L2, TUBA1C, CCDC72,LRWD1, HBD, MSN, GFRA4, CC2D2B, EDF1, AKR7A2, LOC283788, UBA52, RXRA,PTMA, TMEM85, CNP, VPS28, SEC11C, SLC9A3R1, AES, NDOR1, IER2, C2orf14,SMARCA4, SEC61B, TIMM13, NPIP, EMB, ERCC5, TPM4, LRFN1, RAPH1, SRP14,PFDN1, SDF2L1, RPL21, ARRB2, UBC, GDI2, LPXN, LONP1, EIF4A2, ZNF492,HIST1H2AK, SH2D2A, MAL, RPL10, PLSCR3, ZNF430, RPL17, PGAM1, COTL1,FLJ11710, DDX47, YBX1, PRR7, SKAP1, RHBDL1, DCXR, CHCHD2, GLRX, SIX5,RPS7, TIMM8B, MT2A, LOC100130152, GNG2, RNASEH2C, CACNA1E, RAB2A,HIST1H2AG, HNRNPA3, MTPN, LOC113230, CHCHD2, TPT1, MRPL46, ZFP36L2,RPL7A, DNASE1L3, HLA-H, TAF10, IFI27, SERP1, IL32, LOC100127891, EIF3C,GNG11, FAM46C, PTGDS, NINJ1, CACNA1I, MAP7D1, PSME1, C16orf63, PSMD4,RPS10, IK, HMGN2, CDV3, MLL3, NPM1, HCFC1R1, SNRNP70, SKP1, CXXC5, TPM3,NEUROG3, FGF3, RSRC1, CTRB2, SLC25A5, LAT, PHOX2A, LOC100130557, VIM,FAM111A, GAS5, HIST2H3D, FAM101B, FLJ32065, S1PR4, PTTG1, C20orf199,MGEA5, MARCKS, HIST1H4L, DDX39, NPIP, H3F3B, ARHGAP4, HIST1H2BL, SNRPE,TMEM86B, LDHB, ZFAND2B, RPL23A, LOC100290566, NDUFB8, YBX1, ZNF579,COX5A, NDUFB3, EEF1D, RPL12, H3F3A, DEF8, OLA1, GADD45GIP1, LOC644063,FBL, GIMAP1, GLA, LARP1, DBI, ZNF414, NUDT1, EPRS, MPP1, BANK1, FCGRT,MRPL54, C5orf32, ARPC5, LGALS2, SH3KBP1, CAMP, PRIC285, RNASEK,C11orf58, SLC25A39, KPNB1, PPP1CC, EIF3H, TPI1, ABHD2, CCDC104, HOXB13,HIST1H3G, C9orf23, THY1, UBE2F, PPP2R3C, IFIT1, JAK3, RAB31, PSMA5,ASAH2, MAN2A2, RPL26L1, WASF2, SP140, RPL22, DAD1, KLF13, PPP2R5E, OPTN,EML4, PPP2R5A, FNTA, GMIP, NARF, SNX20, ZNF385A, UBE2N, AP3D1, MOBKL2A,ATP5O, TNXB, FAM128B, EEF1A1, COMMD3, SSU72, RPL21, TSPAN5, CGNL1,ATP5I, HMGN2, FGR, SHFM1, TMEM11, CALM3, ISG20, NCRNA00188, NUDT5, CCL4,MAP2K3, HCRT, MAT2B, CXorf18, SLC25A5, HIST3H3, GCN1L1, C15orf63,HIST1H2BC, PPIA, CDKAL1, C17orf96, LGALS3BP, HAX1, RPS18, PPM1K, AKAP13,EIF4G2, BPGM, NCOR1, ARPC1B, COX7C, LCP1, TSPAN10, FTH1, TTC3, RPS13,FAM195A, NDUFA2, C1orf158, OTUD7A, RPS27, GZMA, MRPS31, RPL6, GTF3C6,NCL, MEAF6, MRPL23, RFC1, PSME2, IRF2BP2, CLEC3B, NOP56, NPM1, RPL29,ZNF675, GRIN1, CHMP4B, ATP5H, POLR2J, B3GNT7, IMPDH1, EIF4A1, PSAP,CDC26, ITPKB, SMPD4, C1orf162, FABP5, LTB4R2, PRDX5, YWHAZ, FOXS1,ZNF664, IER5, MAX, MRPL33, RPS12, HLA-DOA, PEBP1, FAM100B, SUGT1, ZMAT2,RNF141, MGLL, EIF5, POTEK, YBX1, SLC25A3, S100A11, HLA-DPA1, GBP4,CCND3, FTH1, LOC440983, UCP2, MTPN, RPL21, RPA3, TSTD1, EEF1B2, RPL35,FAM60A, CD53, CLEC2B, HLA-E, C9orf123, RPL37, MSN, EIF4EBP2, TFF3, BTG1,SPON2, RPL13, PSMB1, CALR, PDE2A, CMC1, RPL21, C12orf35, DCTN1, ELF2,S100A8, SFRS4, RPS24, TOX2, SSB, RPL23AP32, SRP72, RPS27A, HIST1H2BK,SS18L2, PYCARD, ADAR, RPL34, HLA-DMA, CDH22, TOP2B, SDCCAG1, LSM3,RASAL3, UROD, RUFY1, NDE1, SUMO2, BTF3, DYNLL2, XRCC6, PSMC1, AKR1A1,CD2, KIAA0174, MICAL2, AP2M1, IFI27L2, MYEOV2, ATP6AP2, LDHA, ACAA1,LOC442421, PPP1CC, WAC, C17orf90, RPL13A, PA2G4, NACC1, WDFY4, NAT9,CA2, SF3A1, ACAD10, PSMB7, EFCAB4A, CX3CR1, NDUFC2, STARD7, SNRPD2,HIST1H2BM, CFP, TCEAL3, VTI1B, MDH2, LCE1A, C1orf54, ATOX1, DRAM2,C5orf26, RPL31, PPP1R16B, POP4, C16orf53, H3F3A, C21orf33, MESP1, LST1,CALM2, PEX10, PARD6G, SARDH, TAT, HLA-DPB2, RBM27, LOC100288418,LOC100291051, SLC35E4, ATG16L2, C3orf10, TCF3, NR1H3, SNX10, BCAM, NF2,HIST1H1E, LOC100190939, HIST1H2BG, UBE2D3, RPLP1, PLEKHO2, TNR, EXOSC8,LOC100133075, RPAP1, FLJ10357, BIRC3, RPL11, LOC100292388, RPS2P32,MED19, ELFN1, TIMM17A, COX7A2L, PSMB9, DDX24, TADA3, SEMA3B, RPL31,GSK3A, SYNCRIP, MORF4L1, RPL26L1, AP1S2, FYB, C17orf37, C20orf30,LOC729313, FAM119B, CCT8, TSEN54, GABARAPL2, NDUFA8, GPSM3, CIB1, NXT1,C17orf74, CHMP4A, KRT8, CBX3, SLC35B2, DAZAP2, IFI30, BATF, POLD4,LOC100287848, SNX26, EZR, LSM2, CHST13, DDT, EIF3D, ATP5D, GBP6, RPS13,FBXO9, STK40, RBP7, HBA2, NDUFAF2, MT1A, H3F3A, ANKS3, LCE1C, MEX3D,SLA, HADHB, TTRAP, SRGN, RHOC, BOLA1, DOK3, GLIPR2, RPS3, LOC100287521,RPLP1, ERP29, RPL17, HCP5, AHNAK, BMP8B, RPS2P45, LOC401859, MVP, CTBP1,RILP, HLA-DRA, LSM12, RPL23AP7, RPL15, HIST1H3C, ARF3, HMGB2, RPS3A,ZNF24, TYK2, FAM36A, EIF3F, SERBP1, COL27A1, EIF1AY, NUDT13, IAH1,ITSN2, RIC8A, C9orf89, LYSMD2, PSMA1, HN1, FLII, ACTR3, TPM4, UBE2D2,BTBD6, BOLA2B, PPA1, P704P, HEBP1, SURF2, PSMA3, HRK, MX1, PTGES3, MUC2,LOC729082, HBD, NAMPT, NSUN5, WIPF1, TYMP, PDCD10, CSNK1E, IER5, MYL12B,CNPY2, PSIP1, NDUFB9, PSMD4, ACTR10, STRAP, C19orf25, EIF4B, HBG1,FRAT2, MKRN1, CDKN1C, ZNF681, MEG3, ZNF646, TBC1D10C, HOMER3, CAPZA1,CALM3, FLJ43681, AGPAT1, RPIA, RAX2, DDX5, TAF7, ITPK1, FAM102A,DNTTIP1, RPS14, DCTN3, CA1, COPS5, FUZ, CHURC1, CSNK1G2, NDRG2, CNIH4,FAU, ACBD7, LEF1, SRI, EXOC3L2, CIB1, EBF4, RPL26, TCEAL6, HIST1H3A,LOC100129113, HMGN1, DNAJC8, LBX1, FOXC2, HMGB1, POLM, ZNF644, REPS1,C12orf57, TAX1BP1, YBX1, RNF130, NHP2L1, NACA2, PABPC1, MEF2D, RARS2,TSEN34, RPS7P5, NOP58, ZG16B, EIF4B, ATXN7L2, UBE2E3, TPM3, NDUFS6,LOC92659, LZTS2, TUBA4A, CLU, TUBA4A, EEF1G, KIAA1949, SAPS1, FKBP4,NDUFAF3, GLUD1, LGALS1, PRCP, LY86, ERGIC3, AIF1, C3orf10, ATF4,CXorf40B, FAM108A1, SYN1, SF3B1, ATXN2L, PLAC8, ECHS1, C1orf162, HSPE1,TUBB2A, TNFAIP2, NBPF3, RRP7B, MRPL38, MYH9, VASP, ALOX5AP, RPL21P44,HLA-F, OTUD5, GRASP, RPS21, SYNGR4, YWHAG, DSTN, ATP1A1, HIST1H4I,S100A11, C1orf38, TP53TG1, F13A1, DLC1, BAT3, FIBP, HSPA8, C1orf152,LOC100129122, KLHL35, LOC131055, SORL1, SSR2, CBX7, LOC90499, CITED4,RPL13A, CDC42EP5, BCAP31, SEPX1, LYPLAL1, NDUFAB1, ZC3HAV1, PPP1R11,PRKCB, TPM1, WNT6, RNPEPL1, SECTM1, NSA2, CDC42SE2, RAB32, LOC100288252,C3orf26, DUSP15, AMZ2, RPL36A, APRT, SCARA5, CSPP1, VAT1, RHOQ, HPS6,BCR, PSMD1, LAS1L, MIXL1, FBXL17, PKM2, HINT1, GYPC, PYY2, LYNX1, SAP18,ACTC1, FAM107B, HHATL, LCE1A, LOC152217, MRPL21, LOC728723, FIS1,THRAP3, RPS9, CRISPLD2, HEBP2, FCER1G, SPHK2, KRTCAP2, COPE, C10orf104,C18orf23, PFDN5, HIST1H3F, ENO1, OSBPL8, PTPN18, HNRNPA1L2, IDH3B,ANXA6, TST, RHOA, POMP, RPL10L, TOMM20L, HMGN1, PRELID1, GUK1, PTPRCAP,RPLP0P2, C19orf22, LOC646791, TNFAIP8, LOC100192204, CCM2, LST1, MGST3,COPS6, C17orf89, CNOT2, ABLIM1, HSPA4, ZNF254, RPL34, NDUFS8, GLTSCR2,EIF4A1, FOXN2, SMARCD3, CTSB, EDARADD, ERH, TFF3, UBE2V1, CSDA, MLL5,IKZF1, CCL24, LILRA1, CROCCL2, C20orf24, RFTN1, HSP90AA1, ATP6V1G1,MAPK11, FOXO1, HMGN1, FAM45A, HIST1H2AJ, ACTBL2, EVL, TPM1, RASSF5,RRAS, ARHGEF15, NDUFA3, MT1E, HIST1H3E, RPL7, HIST1H2BN, TCOF1, PRAM1,FAM108A1, CASP5, AP1S2, CHCHD1, MT1H, PLEKHJ1, HIST1H4C, MYL12B,FLJ11235, PCK2, RAVER1, TCEAL8, HCST, SUB1, RAB13, FAM162A, ATP5G3,SCNM1, ANXA2, LOC100291560, ZNRD1, HLA-E, NDUFA4, MT2A, HIST1H3H,C19orf56, GNLY, ACTG1, WDR82, RANGRF, RASSF2, PHRF1, MON1B, ST13,SERBP1, AHNAK, ARL6IP4, LOC400061, DEXI, PIP4K2A, C6orf106, ALOX5, JUNB,MEX3D, ZNF56, FAM113B, C20orf30, BUB3, EHD1, GLTSCR2, ZFAND5, RPS5,RPL7A, RPL10, SLC8A1, C19orf33, C11orf17, DNM1P35, RPL23AP7, HBA1,POLR2L, HLA-G, LOC388564, RHPN1, CNTNAP2, UCN2, HNRNPA2B1, SLC2A4RG,KIAA1143, UCP3, SNX3, SSTR3, PFDN5, TUBB6, LOC100288578, MAT2A, PGD,CD36, LOC100289383, CDC2L1, RPL7A, H3F3B, EEF1A1, EIF4H, KRTAP2-4,C22orf9, LST1, GNAI2, HIST1H4J, TMEM149, RNASET2, NDUFS7, ZNF91, NOL7,ZNF714, WASF2, DIAPH1, PF4, COMMD1, C20orf24, H3F3A, RAB1B, RPL19,SNRPF, PF4V1, TRAM2, RPL9, ZNF48, RBM14, BRD2, NAMPT, PAIP2, NET1, SND1,TMEM141, PNKD, NOP56, MYL12A, RPL34, ITGB1BP1, NBPF10, EVI2B, PPDPF,EEF1D, GDNF, NBPF15, FOXP1, SARS, TPM3, KIAA1429, FAM49B, GFAP, ISCA1,INPP5K, HMGB1, SLC22A18AS, PPCS, ATP5J, ZNF706, MBNL1, HIST2H2AB,SUPT4H1, NT5C3, C17orf54, R3HDM2, RHOG, EIF1B, UBOX5, LOC391769, SFRS16,DUX4, CAMLG, ARIH2, RIOK3, ARPC3, ZNF625, UBC, DCAF12, LGALS7B, TIPRL,CAMTA1, CHCHD7, RAB7A, FAM108A1, ID1, FAM117A, ACTG1, POLR3GL, ARAP1,VCP, ABLIM3, YWHAZ, LOC728324, C17orf79, SERPINB1, CEBPD, YPEL3, BAT4,ST13, RPL5, LOC391358, JTB, HIST1H4F, PRDX6, C14orf169, KRTAP2-4,SNRPD1, LOC730256, STRADB, CHCHD10, TSPAN5, H3F3A, HIST1H2BD, LOC391334,ARHGAP9, HIGD2A, DDAH2, RPL13, TCEB2, TCEA1, ATP5A1, MRPL9, CCT5,SEC61B, FABP5, ACTR3, ZNF738, CDK2AP1, ALDOA, RPS28, BEST4, UQCRB, SIK1,ALDH2, CHCHD2, LIMD2, LAT2, C7orf47, CTSS, TOMM7, BBC3, CD48, PARP10,RAB10, FGD3, ARHGEF10L, ZNF92, NPIPL3, RPL29P2, FTL, GPX1, CASC3, MEA1,RPL31, LOC729991-MEF2B, ZNF341, RNF113A, MYCBP2, RPA4, FAM131B, TES,USP10, CECR1, CNFN, GNG10, DUSP6, CNIH, PRDX1, ATPIF1, GALR3, PARK7,LSM10, CMTM6, TXN, KLF2, NSUN5C, LOC100294102, PSMA6, SH3BGRL, BAALC,MALAT1, PABPC3, LOC100128775, CDA, RPL6, MRPL52, MAPRE2, SECISBP2,13-Sep, TUBA1C, HMGB1, SNRPC, RSL1D1, HIST1H3B, LOC440311, AMD1,N4BP2L2, FTHL17, DLGAP3, SLC25A5, HES7, hCG_20426, PRDX2, GDF15, RSU1,FZD9, RWDD1, CLTC, PRPF40A, MED29, C2CD4A, EFHD2, TUSC2, PTP4A2, BECN1,DCAF11, LGALS7, PSMC1, EFNB3, TRAK2, TMEM63B, FKBP2, TAF12, SCAF1,ZNF727, CYB5R3, RPL18, PSMD9, IFITM4P, LOC729406, RBX1, POLR2J2, RPSA,DCAF4L2, GTF3A, ERCC2, USP15, LOC100131482, ACTR3, GIMAP4, EIF3K,HIST2H2AC, FCGR3A, TRAPPC2L, WFDC10B, TRAK2, HIST1H2AC, COX7A2, MRPL53,GSTO1, LOC646890, MAF, FLJ35390, VCP, VAMP8, HIST1H3D, CSDC2, SAT2,RPL21, PDZK1IP1, UBE2R2, C1orf113, CD63, TPM3, BNIP3L, PPIAL4A, HSPB1,RSL1D1, UGP2, RPL27, GPR153, ACAT2, NCAPH, BRI3, WASH2P, PTP4A3,C19orf33, FYB, SNX2, ROBLD3, RPL19P12, HDAC2, LSM3, SERF2, CCT2,APBB1IP, PAX4, RPLP2, LSM8, MDH1, FGD1, DDX54, MAGOHB, ZNF182, SLC4A1,NCRNA00116, SF3B5, CCT6A, HIST1H2BE, CFLP1, EEF1G, HIST1H2BB, CLNS1A,PABPN1, RPA1, LOC100292427, SNF8, SAP18, IL27, SLC34A3, UQCR, NDUFS5,PLAC4, ZCCHC17, ZDHHC22, HIST1H4D, NBR1, C11orf2, ALDOA, HMBOX1, DRD4,RAC2, C6orf62, NDOR1, ROBLD3, ATAD3C, NOP10, SSR2, CCDC88B, GTF2H5,EIF4A2, C10orf84, RPS7, DYNLT1, RPS4X, CT47A11, IER2, NUDT21,LOC100128355, CHP, RPS25, CAT, SMCR5, PSMC6, PDCD4, 7-Sep, HSD17B11,VDAC1, TUBA8, COX4I1, CLEC2D, PPIAL4A, LOC92249, PLIN4, HBA2, NENF,C19orf53, C17orf91, HLA-DMB, CDC42SE1, TMEM14B, CASC3, SNRPG, PRR13,TBX21, SLC44A2, IL7R, SIVA1, CDV3, DHX9, LOC728741, TMEM9B, CSDE1,IFITM2, ALKBH7, TSPYL2, PHB2, ORC6L, TRA2B, EMG1, GSN, OCIAD2, SIGIRR,ATP6V1A, WDR6, LFNG, GNG10, SNRPD3, HSBP1, LIME1, H3F3B, COMMD4, RNF126,ACTG1, CEACAM19, MT1X, COPZ1, HNRNPA1L2, TXNDC17, EIF3F, RPS4Y1, MFNG,CLTA, CCDC57, SPRR2E, FAM65A, AP3S1, UBXN1, RDBP, NSA2, SP110, TXNIP,RNF5, HLA-E, SDHAF1, LOC100129616, UTS2R, PTGES3, RPSA, COX7B, CEBPA,NME1, EID1, STARD8, PRKACB, ATN1, ADA, HNRNPA3, YBX1, URM1, FBXL19,PGK1, CNBP, AURKAIP1, C22orf13, RPL3, EIF3E, RAP1B, FBL, VDAC2,C19orf29, PPID, FAM89B, ARHGEF1, APEH, PCMTD1, CKS1B, RPL13, UQCRH,LOC100129292, POMC, TCF25, PLEKHF1, YWHAZ, RPS10, HIST1H2AJ, ERN1,HNRNPK, NRGN, YWHAZ, PTMA, PDCD6, LAPTM5, LYZ, C1QBP, FDPS, RPS15A,EXOC7, OSTF1, HIST1H2BF, FAM131C, EEF2, HIST1H2AM, MRPL33, SOX1,C4orf48, PRB3, NME2P1, CD37, CTDSP1, COX8A, FAM96A, RASGRP2,RP11-94I2.2, TAOK2, TAF1L, HLA-DPB1, TRIM58, STK4, HSPA8, LOC100288418,UQCRFS1, C7orf28B, SMARCE1, EPAS1, C19orf38, HIST1H4K, EIF3I, STK17B,CDKN1B, ISG15, NDRG1, C20orf141, EEF1A1, RPSA, CCDC115, NKX2-8,RPL13AP3, PPIA, SUSD3, ATP5J2, ZNF100, C6orf1, C7orf28A, CGGBP1, FLOT1,HSF1, KLF16, WAC, SCLT1, AMD1, UBXN6, UBE2F, SEC13, SSBP1, ZDHHC4,SERF2, RPS6, LRRC2, ENO1, ANXA2, CYTH4, RHOA

TABLE 21 Pathway Expression in Total cMVs Pathway Members AndrogenGTF2F1, CTNNB1, PTEN, APPL1, GAPDH, Receptor CDC37, PNRC1, AES, UXT,RAN, PA2G4, (AR) JUN, BAG1, UBE2I, HDAC1, COX5B, NCOR2, STUB1, HIPK3,PXN, NCOA4 EGFR1 RALBP1, SH3BGRL, RBBP7, REPS1, SNRPD2, CEBPB, APPL1,MAP3K3, EEF1A1, GRB2, RAC1, SNCA, MAP2K3, CEBPA, CDC42, SH3KBP1, CBL,PTPN6, YWHAB, FOXO1, JAK1, KRT8, RALGDS, SMAD2, VAV1, NDUFA13, PRKCB1,MYC, JUN, RFXANK, HDAC1, HIST3H3, PEBP1, PXN, TNIP1, PKN2

In a related set of experiments, expression profiling was performed inPCSA+cMVs. PCSA+cMVs were isolated using immunoprecipitation as inExample 32. Expression was performed as above using Agilent Whole Genome44K microarrays. 2402 mRNAs were found in the PCSA captured samples,including those shown in Table 22. The TNF-alpha pathway was the mostsignificantly overexpressed pathway. The members of the TNF-alphapathway are shown in Table 23.

TABLE 22 mRNAs Expression in PCSA+ cMVs LOC100132006, EHMT2, RPL23,RPS13, HDDC3, LOC150759, MEGF11, CRCP, LRP1, CDH6, C9orf30, MAB21L2,EPHA2, SYT2, BOK, NLE1, C2orf53, ORMDL3, TUT1, CYP2E1, C6orf81, GATAD2A,RPL18, C3orf21, MASP1, CLOCK, CENPP, NFKBIB, LOC729915, C17orf64, BLK,NR1H2, SMARCA4, ACVRL1, ARFIP1, NFKB2, tcag7.1196, JUN, LOC100128760,ZFYVE19, HLA-DRB5, NDUFB9, MFN1, CLK1, LOC100289600, SULT1A2, BTF3L1,IGSF10, RALY, KLK3, KIAA1751, RUVBL1, DNAJC3, C14orf166, BCAP31, HNRNPU,DFNB31, CENPBD1, WNK2, PNLIPRP1, OAZ1, GEMIN5, C19orf55, CHRDL1,CACNA1B, LOXL4, HIRIP3, hCG_1643808, COX4I2, FABP3, GAPDH, TSSC1,GABARAPL2, EXO1, POU6F2, STX8, HSP90AA1, TNFRSF11B, SPACA5, TNRC18,SAP30BP, FOXK2, RPL23AP53, PIK3R4, XPC, SOCS7, RPL35A, UBC, NKG7, SNCA,PTK2B, PPIA, LOC100289350, CDKN2B, TNNI2, MUC5B, MED6, NOL8, HS2ST1,SNRPC, LOC100131582, DNAJA1, RPL10, RPL10, SYCE1L, RPS25, PNMAL1, RPS2,CDKN2A, LOC100288578, CFD, LOC100134569, CD52, NLRC5, OAZ1, DCI, RPL23A,LSP1, RPL39, VTA1, RPS29, MLXIPL, FAM133B, UTF1, HBQ1, SSR4, HLA-DRB3,NOS3, L1CAM, WHAMM, PRR13, IGF1, GPR61, IL26, CCDC69, RPL35, TFE3, RPL4,FAM128B, PAK1IP1, RPS10, FBRSL1, MEIS1, DYNLRB1, ISCU, PRR5, FCGR2A,DNAI2, EPSTI1, TNRC6B, RPL36, NCOA4, XRN1, RPL14, EEF1D, RPS10,LOC388152, TRIM55, SPATA2L, FLJ43681, TSSC4, HIST1H2AD, JMJD6, TCF7L2,RPSA, PMEPA1, PRR13, SIRPG, ANKK1, MCTS1, TCL1A, HLA-A, ALDH3B1, POLD4,ACTB, SDK1, RPL38, SEC62, CASZ1, EVPL, ZNF784, DEPDC6, ZNF638, RPL23AP7,COMMD7, SMARCC2, RPL36AL, PHF21A, RPL10A, OR2H1, ATAD3A, C10orf82,RPS15, CAP2, CARD16, ZDHHC16, FPR1, ETFB, NPPC, BAX, IFI27, NYX,SLC27A1, LOC100133280, CAPN10, C11orf67, ACRBP, TERT, NDUFA6, RPL30,TNRC4, NDUFA4, ERBB2, OAZ1, RPS3, TPSG1, FAM43B, C16orf11, SIRPA,PABPC1, FAM73B, HMOX1, RPS10P7, GNAS, HPD, NEXN, SPARC, RASL10B,LOC100293539, TMTC4, C21orf91, GMPR, ADAMTS13, VDR, SRRM3, MYPOP, FTH1,BLOC1S1, UBE2L3, APP, RPSA, SOD1, CARD8, NACA, NCRNA00152, HTR1F, SUMO2,PHLDB3, H3F3C, PVALB, LOC286272, SCLT1, C9orf131, MTMR14, RNF44,HLA-DPB1, TP63, FGD3, RPS27, LOC648771, TMEM158, POLD3, RPSA, PEX1,USP33, POLRMT, RPS29, FXYD5, RALGDS, BTRC, ZCCHC6, THEM5, RPL23, VAX2,TMSB10, MMP28, HMBS, GNB2L1, COX6B1, UBB, CASP8, CCS, LCE3E, RPL14,MRPL38, RPL3, RPL13, SYMPK, EEF1D, DNMT3A, PCBP1, FHIT, LCE1D, KCNQ1DN,HRASLS5, SYT15, LOC643668, TPT1, RPS15, SNHG5, RPL9, DNAJC4, MYCNOS,RPL21, EGLN3, TUBG1, SNRPB, FLJ22184, RPL32, ASCC3, ZNF2, HCN2, B2M,PKM2, COX6A2, NACA, CCL5, RPL37A, PRM3, TTC1, DYNLL1, EEF1G, ACOT13,PSMB6, HBG1, LCE5A, BAX, LOC284998, RPS17, RPL10, TRIM24, IMP5, RPS25,RPL23AP82, SMARCA2, RPL24, PRELID1, RPS19, RPL26, TRMT112, RPL21,LOC100129917, CCNI, TMSL3, TMEM140, C6orf70, CA5A, POLR2J, C6orf48,LOC100128731, DLAT, PCBP1, MIA2, REEP5, SH3BGRL3, RPL29, HIST3H2A,RPL37, THUMPD1, APLNR, LOC100288331, SEC14L2, EXOC1, LPIN3, ZNF592,NPHS2, FANCM, RP3-377H14.5, FAM124A, S100A13, IFITM1, RPL12, IGF2, FTH1,RPL29, MAP3K6, CDC2L1, ING5, BBC3, RPS8, CD79A, LOC100129291, RPLP0,EIF3K, LOC100293090, RPS7, RABEP1, RAB8A, RCOR2, LOC220115, VIM, IFITM5,NBPF10, S100A12, COX5B, PPP1R14A, CD48, HSPB1, GLTPD1, RPL3, RPS2,RPS3A, LCE2A, CLIP3, DAB1, MTPN, SCARF2, CD4, IL12RB2, ARPC2, RPS15A,EVX1, C19orf71, YWHAE, SNHG8, TBCA, KIAA0125, HIST1H4E, ACTB, EEF1D,TNNT2, RPS28, ZNF761, HDAC7, RPSAP52, PRICKLE3, BAG5, LOC644950, PHLDA1,RPLP0, UCRC, PALMD, RPL18A, HBB, GRIN3B, ATP5G2, MAFA, C14orf162,EEF1A1, SLC25A6, FAU, NDUFS7, SLK, COL6A2, SYNPO, RPL23A, UBA52, MYL6,COMMD6, HOXA3, GPR132, PLEKHN1, BST1, SURF1, CDC2L5, RPS16, ADAMTS7,MON1B, C10orf47, POLR2A, RPSA, TAOK3, ZC3H6, HIST1H1C, RPS2P32, RPS27A,RPL18A, MEX3D, POLR2E, 5-Sep, RPS20, SHISA9, ALX1, RPS4P16, MIF, RPS26,PAX9, LOC642031, LOC100289600, SF3A2, CCDC88C, RPL14, USMG5, RPL17,VPS18, PFKFB3, KCNK15, LOC728449, RPS3A, TOMM7, ALAS2, ZBTB46, GRIN2D,RPL8, NEDD8, FAHD1, KLHL34, IK, GMFG, GNAZ, GOSR1, SEPW1, SCRT2,LOC100288165, CCDC24, C16orf81, UBL5, RYBP, TNRC18, NKX1-2, SUPT4H1,ATP5I, RPLP0, EN2, BZRAP1, SDK2, RAB8A, RPL34, MXD4, FAM63B, UBE2S,ATP5D, MRGPRF, CD99, BAG1, POLD1, POLR2L, CDC2L1, RAC2, SIRT3, NPM1,RPS2, DDX49, LOC649294, URG4, TAPT1, EIF1, MAN1B1, ARHGEF11, ATP6V0C,C1orf175, PLEKHO1, HCLS1, LSMD1, NFE2L1, C11orf10, UBC, LEPROT, CEL,HIST1H1D, SFRS8, HIST2H2AC, RPL37A, MED13L, PPIAL4A, FCRL2, RPL35,KRTAP1-3, LOC440461, S100A6, SOD2, PAX6, SAPS1, FAM129B, LIPE, NME2,FLJ23867, KLF14, RPS11, HCN4, PAX8, CSTA, ZNF713, POTEF, RPS14, FTL,FOXD3, MXD1, RPL35, HYAL1, ZNF506, ATF6B, CRIP1, ZNF467, IFI16,RABGAP1L, ANO7, CGB1, PTRF, LOC100131262, PPBP, SNX19, PTMA, HBM,LOC341056, SERPINB1, RPS10, C17orf88, CFL1, RPL23A, TUBA1C, VDAC3,HSPA8, TP53TG3, RGS10, BCAM, PFDN6, EEF1D, TMEM201, PABPC1, OGDH, RPL34,NNAT, RSRC2, LOC730144, RPL27A, ZNHIT1, TALDO1, FOXQ1, LRRC6, BTF3,ARL6IP4, MEPE, C15orf21, LENG8, N4BP3, LGR4, GJC1, FAM128B, IRX5,A4GALT, CTSA, PPIA, RALBP1, TAF3, LOC541471, MMP11, ADAMTS10, IL11,C9orf167, FLJ31356, RTN3, NIN, RYR3, YLPM1, PPIAL4A, OR2H1, RPS3A,LOC389641, FAM177A1, MAGEE1, CYP2W1, HEMGN, ZFPM1, HIST1H2BO, RRAS,RPS3A, EIF3M, PTMA, EIF3D, TAGLN2, LMOD1, CASP4, GZMB, NGFRAP1, RPS17,AGAP3, SOX4, RPS5, NDUFB2, PCMTD1, EIF1, C19orf73, SIK1, PSMB10, ROMO1,CD86, RPS10, FAM154A, HILS1, NCOA4, ATP5L, LOC100288418, MDFI, EEF1B2,A2ML1, OSMR, DLX1, SOD1, SEC62, RPL12, LOC100130331, RNF151, VSIG10L,NDUFA1, RPS26, JMJD8, LOC283177, LTA4H, CYP2F1, DIRC1, C1orf27, TRIM10,SUMO2, HLA-B, GH1, VAMP2, TNXB, LOC100288755, SUPV3L1, SPEF1, tcag7.907,RPS19, HIST3H2BB, RSPH10B, TBX3, RPS10, UQCRQ, hCG_19809, RPL13A, ZFR2,RHOBTB1, RPL21, MAX, CAMKK2, PDZD7, DCAF10, FTL, DEFA3, IQSEC2, NRG4,GIPR, GNAS, RELB, ITIH2, CASP4, S100A4, OGFR, RPLP0P3, CCDC93, HMGB1,RPL36A, PPIA, NDUFA1, TUBA4A, TUBA1B, SCD5, HIST2H2AA4, SAFB, PTMS,BLVRB, HIST1H2AM, FTH1, RPL29, STEAP4, RPL15, TMIGD2, LTB, APOC4,HNRNPA1, SLC12A7, HLA-DOB, RPL9, GGT6, ZNF525, SLC8A2, EN1, PKN2, KRT16,ODF3L2, BAX, NFE2L1, CCDC50, TPT1, CKB, IFITM3, LOC399851, UXT, NAB2,DYNLL1, TUBB1, SOX3, RPL21, GUK1, CHD7, RPS2P32, GCET2, GRAP, SPSB4,GSTP1, UBE2G2, HIST1H2AH, VCX3A, SERGEF, DUSP9, SMEK1, FCRLB, ECHDC2,MTA1, SAFB, CREB3L3, LOC119358, DRAP1, TMEM175, RPL21, RPL21P44, LRP3,FAU, MOGAT1, DYRK4, TYROBP, RPL22L1, C12orf40, PTGR2, SLC46A1, LCE1F,MORN1, PALM2-AKAP2, COX6C, RPL41, ALOX15B, MYL6, RGS18, C11orf31,C18orf32, CUL1, ARHGDIB, MPPED1, NPM1, ATP5E, LOC648771, TNXB,HIST1H2AE, ACTB, CCDC62, RPS26, H2AFJ, TMSB4X, LOC151009, RPL30,RPL23AP71, HIST2H3D, BID, AGRP, RPL28, ZNF219, FXYD5, GPR149, MGC10814,RPL39, GZMH, GPR150, PTMA, RPS3A, CEND1, CYB561D1, POU5F1P4, UBB,SPPL2B, CLDN5, GBP4, HLA-B, CASKIN1, TMSL3, ZNF746, NFYA, VGLL2, ODAM,ADAMTSL5, DPEP3, PSPH, ALPPL2, GRN, NPAS3, SLAIN2, ADRA2C, NPM1,C14orf2, COX6A1, PRNP, ATP5E, RPL7, PRR24, CDCA3, CXorf18, HNRNPA1,RPL10A, HIST1H2BH, BCLAF1, hCG_2014417, TMEM30B, GNAZ, RPL7A, ANAPC11,C21orf81, PRKCG, TMED10P, C6orf25, S100A9, NDUFB10, WNT2B, 9-Sep, ACTB,CRTC1, ZNF157, SSX2, WNT10A, EHD2, SSTR2, RPS23, HSPB1, RHO, TMEM111,GSTK1, LOC100132247, C16orf93, XRCC6, CCNT1, NDUFA2, NDUFB4, RPS14,CTTN, RPL34, TMEM191B, H2AFJ, TRIM29, EEF1D, UBA52, HLA-C, LOC729732,EXOC3L2, CCDC72, HBD, EDF1, UBA52, PTMA, VPS28, AES, NDOR1, IER2,C2orf14, SMARCA4, ZNF575, LRFN1, SRP14, RPL21, UBC, LPXN, TMIE,HIST1H2AK, ID4, RPL10, RPL17, PRR7, CHCHD2, SIX5, RPS7, TIMM8B, MT2A,LOC100130152, FABP6, SCNN1D, MTPN, TPT1, RUVBL1, RPL7A, HLA-H, IL32,EIF3C, GNG11, CACNA1I, PSME1, RPS10, MLL3, HCFC1R1, SNRNP70, FGF3,RSRC1, MSRA, PHOX2A, VIM, GAS5, HIST2H3D, C20orf199, HIST1H4L, H3F3B,HIST1H2BL, ZNF658, TMEM86B, LDHB, RPL23A, LOC100290566, ZNF579, EEF1D,RPL12, H3F3A, FBL, DBI, ARPC5, LGALS2, LIG3, C11orf58, EIF3H, HOXB13,NRN1, RAB31, ASAH2, EDNRB, RPL26L1, RPL22, CACNB2, AP3D1, ATP5O, TNXB,EEF1A1, RPL21, ATP5I, HMGN2, CALM3, ISG20, NCRNA00188, DCAF8, CXorf18,HIST3H3, CDKAL1, LOC338864, C17orf96, RPS18, COX7C, LCP1, TSPAN10, FTH1,RPS13, VARS2, RPS27, FTSJ2, RPL6, PSME2, RPL29, SMPD4, C1orf162, LTB4R2,YWHAZ, FOXS1, MAX, RPS12, SOX11, ITGAX, YBX1, SLC25A3, HLA-DPA1, FTH1,RPL21, KCNAB3, SSX5, UTP14A, EEF1B2, RPL35, HLA-E, RPL37, KRT77, RPL13,PSMB1, RPL21, S100A8, RPS24, RPS27A, HIST1H2BK, RPL34, CDH22, RUFY1,BTF3, GUCA1B, IFI27L2, MYEOV2, RPL13A, NCRNA00181, NACC1, LOC344967,CA2, ACAD10, SNRPD2, LCE1A, LOC90246, NPM2, H3F3A, MESP1, LST1, CALM2,CASZ1, PEX10, LRRC18, PARD6G, TAT, RBM27, LOC100288418, LOC100291051,SLC35E4, C3orf10, PIAS1, BCAM, FAM55A, LOC100190939, RPLP1, RPL11,LOC100292388, RPS2P32, ELFN1, SEMA3B, RPL31, ADAMTS13, PHF10, LOC729141,DIDO1, C17orf74, TRPS1, SLC35B2, IFI30, POLD4, LOC100287848, CYSLTR1,SNX26, EIF3D, GBP6, RPS13, HBA2, MT1A, H3F3A, LCE1C, MEX3D, RPS3,KIAA0368, RPLP1, ERP29, RPL17, BMP8B, LOC401859, RPS3A, BOLA2B, P704P,HRK, MUC2, HBD, MYL12B, NDUFB9, HBG1, MKRN1, TBC1D10C, FLJ43681, AGPAT1,RAX2, PAK6, FLYWCH2, RPS14, FUZ, ACTR8, TTC17, LPPR5, FAU, ACBD7,EXOC3L2, RPL26, HIST1H3A, DDN, LBX1, FOXC2, C12orf57, LOC642826, NACA2,PABPC1, RPS7P5, ATXN7L2, LOC92659, TUBA4A, TUBA4A, EEF1G, FKBP4,NDUFAF3, LGALS1, AIF1, ATF4, SYN1, RALYL, ATXN2L, C4orf31, MRPL38,RPL21P44, OTUD5, ADAMTSL5, GRASP, RPS21, POM121L8P, PLEKHA6, C1orf38,HSPA8, LOC100129122, KLHL35, TCF25, ZNF365, RPL13A, CDC42EP5, WNT6,RNPEPL1, LOC100288252, DUSP15, RPL36A, MIXL1, C19orf77, FBXL17, KLHL22,HINT1, LYNX1, HHATL, BARHL2, MRPL21, RPS9, FCER1G, C18orf23, PFDN5,RPL10L, TOMM20L, HMGN1, GUK1, PTPRCAP, RPLP0P2, LST1, ZNF254, RPL34,ERH, CCL24, CROCCL2, PDE6C, DDX31, NDUFA3, FAM71B, HIST1H2BN, ZC3H13,PCDH17, MT1H, ETV5, HIST1H4C, MYL12B, FLJ11235, PCK2, RAVER1, HCST,SCNM1, ANXA2, LOC100291560, NDUFA4, MT2A, KIF19, PELI3, ACTG1, MON1B,BANP, ARL6IP4, MEX3D, VPS13D, GLTSCR2, RPS5, RPL7A, RPL10, SLC8A1,DNM1P35, RPL23AP7, HBA1, POLR2L, HLA-G, TNFAIP8L3, PTHLH, TOE1, RHPN1,UCN2, UCP3, PFDN5, LOC100288578, IRGC, LOC100289383, RPL7A, EEF1A1,KRTAP2-4, GSTT1, FAM178A, RNASET2, GATS, PF4, H3F3A, RPL19, TRAM2, RPL9,NET1, MYL12A, RPL34, ORAI1, CCDC11, PPDPF, EEF1D, GDNF, TPM3, C20orf151,OAS3, AZU1, SLC22A18AS, HIST2H2AB, C17orf54, DPP6, R3HDM2, TSPAN33,C20orf201, LOC391769, SFRS16, DUX4, ARPC3, UBC, LGALS7B, TCOF1, PGM5,ACTG1, YPEL3, NR2C2AP, RPL5, PRDX6, C14orf169, HCG18, H3F3A, LOC391334,CHST10, MAP6D1, RPL13, C6orf182, TCEB2, MPHOSPH8, FABP5, ZNF48, ALDOA,RPS28, KCNQ4, GCGR, UQCRB, SIK1, DNMT1, PPAN, TOMM7, PARP10, CDC34,RPL29P2, FTL, GPX1, RPL31, FAM131B, CNFN, GALR3, TXN, BAALC, ALKBH2,CDA, RPL6, MRPS22, LOC440311, FTHL17, DLGAP3, HES7, FZD9, RWDD1,ANKRD50, SCAMP5, CT47B1, GATA3, DCAF11, JAK3, GRM4, LGALS7, EFNB3,SCAF1, ZNF727, PLEKHG4B, GTF2H1, CYB5R3, RPL18, LOC100134359, PSMD9,RBX1, POLR2J2, RPSA, DCAF4L2, FAM163A, RSHL1, IGFBP3, EIF3K, HIST2H2AC,WFDC10B, LOC100130811, USP30, COX7A2, MAF, VAMP8, CSDC2, RPL21,C1orf113, SGK269, BNIP3L, PPIAL4A, RPL27, GPR153, NCAPH, BRI3, NDUFAF2,WASH2P, NID2, C19orf33, RHBG, RPL19P12, SERF2, PAX4, PPARGC1B, RPLP2,LOC440181, FGD1, C15orf37, ZNF182, SLC4A1, GOLGA6L10, SF3B5, HIST1H2BE,EEF1G, MITF, LOC100292427, UQCR, NDUFS5, ZDHHC22, DRD4, RAC2, NDOR1,SSR2, C10orf84, PHF7, RPS7, RPS4X, USP6, LOC440330, DRAM1, SNX15, RPS25,TUBA8, COX4I1, LOC92249, MYBL1, PLIN4, HBA2, C17orf91, TMOD4, PRR13,CDV3, CSDE1, IFITM2, TAF1, SCTR, PHB2, MYH6, FUZ, TCEAL7, LIME1, IL21,MAN1C1, H3F3B, C1orf170, GGT1, CEACAM19, HNRNPA1L2, ZFAND2B, ZNF467,UBXN1, OSBPL10, RGNEF, SP110, HLA-E, AZI2, SDHAF1, MAPK13, H1FNT, DAP,C16orf82, RPSA, SPRN, STARD8, ATN1, TPTE2, RPL3, EIF3E, FBL, ALPL, DKK4,ARHGEF1, TNFRSF25, PCMTD1, C21orf93, RPL13, UQCRH, LOC100129292, SKIL,WHSC1L1, RPS10, EDEM2, NRGN, IFT57, FOXA3, RUNDC2C, PTMA, NRXN1, TCEA3,RPS15A, FAM167B, EXOC7, HIST1H2BF, HMGA2, FAM131C, SIRPD, HIST1H2AM,AIG1, TTLL5, FTCD, SOX1, ZNF138, PRB3, LOC346329, NME2P1, CTDSP1,C14orf126, COX8A, LOC26102, PSCA, TAF1L, HLA-DPB1, MYST4, ORC3L, SSX9,HSPA8, RGS12, LOC100288418, HEY2, PCSK4, SOBP, TMEM232, RGS19, ATP2B2,NTN1, C10orf35, PI4KAP2, LOC100287114, C1orf95, HADH, C20orf141, DSCR4,SEMG2, EEF1A1, SCRT1, CYB5A, RPSA, KIN, ST3GAL4, NKX2-8, RPL13AP3,FGF17, PPIA, SAA2, SLC37A1, MYST4, DDA1, PDE1C, CGGBP1, SLC23A3, KBTBD5,FLOT1, HSF1, BAT2D1, KLF16, AMHR2, WAC, EPB41L4A, ETFDH, TNN, SLURP1,CELA3B, LOC100272216, KLF1, TRPC4, D21S2091E, RBBP8, SSBP1, KCNH6, GRK4,FIBCD1, SERF2, RPS6, LRRC2, ENO1, DHDDS, C1orf226

TABLE 23 Pathway Expression in PCSA+ cMVs Pathway Members TNF-alphaBCL3, SMARCE1, RPS11, CDC37, RPL6, RPL8, PAPOLA, PSMC1, CASP3, AKT2,MAP3K7IP2, POLR2L, TRADD, SMARCA4, HIST3H3, GNB2L1, PSMD1, PEBP1, HSPB1,TNIP1, RPS13, ZFAND5, YWHAQ, COMMD1, COPS3, POLR1D, SMARCC2, MAP3K3,BIRC3, UBE2D2, HDAC2, CASP8, MCM7, PSMD7, YWHAG, NFKBIA, CAST, YWHAB,G3BP2, PSMD13, FBL, RELB, YWHAZ, SKP1, UBE2D3, PDCD2, HSP90AA1, HDAC1,KPNA2, RPL30, GTF2I, PFDN2

The genes in Table 24 were all significantly downregulated in PCSA+cMVsas compared to the total cMV population. Expression was compared using at-test with Benjamini and Hochberg false-discovery rate correction.Significantly differentially expressed mRNAs are shown in the table(corrected p-value≦0.05).

TABLE 24 mRNAs downregulated in PCSA+ cMVs compared to total cMVs RPL23,RPS13, RPL18, NDUFB9, BTF3L1, KLK3, C14orf166, OAZ1, GAPDH, GABARAPL2,HSP90AA1, TNRC18, RPL23AP53, RPL35A, UBC, NKG7, SNCA, PPIA, HS2ST1,RPL10, SYCE1L, RPS25, RPS2, CD52, OAZ1, DCI, RPL23A, LSP1, RPL39, RPS29,HBQ1, SSR4, WHAMM, RPL35, RPL4, FAM128B, RPS10, FBRSL1, ISCU, PRR5,RPL36, NCOA4, RPL14, EEF1D, RPS10, HIST1H2AD, RPSA, PMEPA1, ANKK1,TCL1A, POLD4, ACTB, RPL38, ZNF784, RPL23AP7, SMARCC2, RPL36AL, RPL10A,RPS15, IF127, NYX, SLC27A1, NDUFA6, RPL30, NDUFA4, OAZ1, RPS3, TPSG1,PABPC1, HMOX1, RPS10P7, GNAS, LOC100293539, MYPOP, FTH1, BLOC1S1, RPSA,SOD1, NACA, SUMO2, H3F3C, HLA-DPB1, RPS27, LOC648771, TMEM158, RPSA,RPS29, RALGDS, RPL23, TMSB10, GNB2L1, COX6B1, UBB, CASP8, RPL14, RPL3,RPL13, PCBP1, FHIT, LCE1D, HRASLS5, TPT1, RPS15, SNHG5, RPL9, RPL21,FLJ22184, RPL32, ZNF2, HCN2, COX6A2, NACA, RPL37A, DYNLL1, EEF1G, HBG1,LCE5A, RPS17, RPL10, RPS25, RPL23AP82, RPL24, PRELID1, RPS19, RPL26,TRMT112, RPL21, CCNI, TMSL3, C6orf48, PCBP1, SH3BGRL3, RPL29, HIST3H2A,RPL37, RP3-377H14.5, IFITM1, RPL12, FTH1, RPL29, BBC3, RPS8, RPLP0,EIF3K, RPS7, RCOR2, VIM, IFITM5, NBPF10, S100A12, COX5B, CD48, HSPB1,GLTPD1, RPL3, RPS2, RPS3A, MTPN, ARPC2, RPS15A, EVX1, SNHG8, TBCA,HIST1H4E, ACTB, EEF1D, RPS28, RPSAP52, LOC644950, RPLP0, UCRC, RPL18A,HBB, ATP5G2, EEF1A1, SLC25A6, FAU, NDUFS7, RPL23A, UBA52, MYL6, COMMD6,HOXA3, RPS16, ADAMTS7, RPSA, ZC3H6, HIST1H1C, RPS2P32, RPS27A, RPL18A,MEX3D, RPS20, RPS4P16, MIF, RPS26, LOC642031, SF3A2, RPL14, USMG5,RPL17, VPS18, KCNK15, LOC728449, RPS3A, TOMM7, ALAS2, GRIN2D, RPL8,NEDD8, GMFG, SEPW1, LOC100288165, C16orf81, UBL5, NKX1-2, ATP5I, RPLP0,SDK2, RPL34, UBE2S, ATP5D, BAG1, POLD1, POLR2L, CDC2L1, RAC2, NPM1,RPS2, LOC649294, EIF1, ATP6V0C, PLEKHO1, HCLS1, LSMD1, NFE2L1, C11orf10,UBC, HIST1H1D, HIST2H2AC, RPL37A, PPIAL4A, RPL35, KRTAP1-3, S100A6,SOD2, SAPS1, FAM129B, NME2, FLJ23867, RPS11, HCN4, CSTA, ZNF713, POTEF,RPS14, FTL, FOXD3, RPL35, CRIP1, ZNF467, PTMA, HBM, SERPINB1, RPS10,CFL1, RPL23A, TUBA1C, HSPA8, RGS10, BCAM, EEF1D, TMEM201, PABPC1, OGDH,RPL34, LOC730144, RPL27A, ZNHIT1, TALDO1, FOXQ1, BTF3, ARL6IP4,C15orf21, LGR4, FAM128B, IRX5, PPIA, RTN3, PPIAL4A, RPS3A, MAGEE1,ZFPM1, HIST1H2BO, RRAS, RPS3A, EIF3M, PTMA, EIF3D, TAGLN2, CASP4, GZMB,RPS17, AGAP3, RPS5, NDUFB2, PCMTD1, EIF1, C19orf73, PSMB10, ROMO1, CD86,RPS10, NCOA4, ATP5L, EEF1B2, SOD1, RPL12, LOC100130331, VSIG10L, NDUFA1,RPS26, LTA4H, SUMO2, HLA-B, LOC100288755, RPS19, RPS10, UQCRQ,hCG_19809, RPL13A, RPL21, PDZD7, FTL, DEFA3, IQSEC2, GIPR, GNAS, CASP4,S100A4, OGFR, RPLP0P3, HMGB1, RPL36A, PPIA, NDUFA1, TUBA4A, TUBA1B,HIST2H2AA4, BLVRB, FTH1, RPL29, RPL15, LTB, HNRNPA1, RPL9, GGT6, ZNF525,PKN2, NFE2L1, TPT1, CKB, IFITM3, UXT, DYNLL1, SOX3, RPL21, GUK1,RPS2P32, GSTP1, HIST1H2AH, DUSP9, FCRLB, LOC119358, DRAP1, TMEM175,RPL21, RPL21P44, FAU, TYROBP, RPL22L1, LCE1F, PALM2-AKAP2, COX6C, RPL41,MYL6, C11orf31, ARHGDIB, NPM1, ATP5E, LOC648771, TNXB, HIST1H2AE, ACTB,RPS26, H2AFJ, TMSB4X, RPL30, RPL23AP71, HIST2H3D, BID, RPL28, ZNF219,FXYD5, MGC10814, RPL39, GPR150, PTMA, RPS3A, CYB561D1, UBB, SPPL2B,HLA-B, CASKIN1, TMSL3, ZNF746, DPEP3, PSPH, NPAS3, NPM1, C14orf2,COX6A1, ATP5E, RPL7, PRR24, HNRNPA1, RPL10A, HIST1H2BH, RPL7A, ANAPC11,S100A9, NDUFB10, 9-Sep, ACTB, CRTC1, RPS23, HSPB1, RHO, XRCC6, NDUFA2,NDUFB4, RPS14, RPL34, TMEM191B, EEF1D, UBA52, HLA-C, EXOC3L2, CCDC72,HBD, EDF1, UBA52, PTMA, VPS28, IER2, SMARCA4, SRP14, RPL21, UBC,HIST1H2AK, RPL10, RPL17, PRR7, CHCHD2, RPS7, TIMM8B, MT2A, LOC100130152,MTPN, TPT1, RPL7A, IL32, EIF3C, CACNA1I, PSME1, RPS10, MLL3, FGF3,PHOX2A, VIM, GASS, HIST2H3D, C20orf199, HIST1H4L, H3F3B, HIST1H2BL,LDHB, RPL23A, ZNF579, EEF1D, RPL12, H3F3A, FBL, DBI, ARPC5, LGALS2,C11orf58, EIF3H, RPL22, AP3D1, ATP5O, EEF1A1, RPL21, ATP5I, HMGN2,ISG20, NCRNA00188, HIST3H3, CDKAL1, C17orf96, RPS18, COX7C, LCP1,TSPAN10, FTH1, RPS13, RPS27, RPL6, PSME2, RPL29, C1orf162, YWHAZ, RPS12,YBX1, SLC25A3, HLA-DPA1, FTH1, RPL21, ELF1B2, RPL35, HLA-E, RPL37,RPL13, PSMB1, RPL21, S100A8, RPS24, RPS27A, HIST1H2BK, RPL34, RUFY1,BTF3, IFI27L2, MYEOV2, RPL13A, NACC1, SNRPD2, LCE1A, H3F3A, MESP1, LST1,CALM2, PARD6G, LOC100291051, SLC35E4, C3orf10, BCAM, RPLP1, RPL11,LOC100292388, RPS2P32, ELFN1, RPL31, C17orf74, IFI30, POLD4,LOC100287848, SNX26, EIF3D, GBP6, RPS13, HBA2, MT1A, H3F3A, RPS3, RPLP1,RPL17, LOC401859, RPS3A, BOLA2B, P704P, HRK, HBD, MYL12B, NDUFB9, HBG1,MKRN1, TBC1D10C, FLJ43681, RAX2, RPS14, FAU, ACBD7, RPL26, HIST1H3A,LBX1, C12orf57, NACA2, PABPC1, RPS7P5, TUBA4A, TUBA4A, EEF1G, NDUFAF3,LGALS1, AIF1, ATF4, ATXN2L, MRPL38, RPL21P44, RPS21, C1orf38, HSPA8,LOC100129122, RPL13A, CDC42EP5, WNT6, LOC100288252, RPL36A, HINT1,LYNX1, MRPL21, RPS9, FCER1G, C18orf23, PFDN5, RPL10L, HMGN1, GUK1,RPLP0P2, LST1, ZNF254, RPL34, NDUFA3, MT1H, HIST1H4C, MYL12B, RAVER1,HCST, ANXA2, LOC100291560, NDUFA4, MT2A, ACTG1, ARL6IP4, MEX3D, GLTSCR2,RPS5, RPL7A, RPL10, DNM1P35, HBA1, POLR2L, HLA-G, UCP3, PFDN5, RPL7A,EEF1A1, KRTAP2-4, H3F3A, RPL19, RPL9, NET1, MYL12A, RPL34, PPDPF, EEF1D,GDNF, TPM3, HIST2H2AB, R3HDM2, LOC391769, SFRS16, DUX4, ARPC3, UBC,ACTG1, RPL5, PRDX6, H3F3A, LOC391334, RPL13, TCEB2, ALDOA, RPS28, UQCRB,SIK1, TOMM7, PARP10, RPL29P2, FTL, GPX1, RPL31, GALR3, TXN, BAALC, RPL6,LOC440311, DLGAP3, HES7, ZNF727, RPL18, PSMD9, POLR2J2, RPSA, EIF3K,HIST2H2AC, COX7A2, VAMP8, RPL21, C1orf113, BNIP3L, PPIAL4A, RPL27,GPR153, BRI3, WASH2P, RPL19P12, SERF2, PAX4, RPLP2, SF3B5, HIST1H2BE,EEF1G, UQCR, NDUFS5, DRD4, RAC2, NDOR1, SSR2, RPS7, RPS4X, RPS25,COX4I1, HBA2, PRR13, CDV3, CSDE1, IFITM2, PHB2, H3F3B, HNRNPA1L2, UBXN1,HLA-E, RPSA, RPL3, EIF3E, FBL, RPL13, UQCRH, LOC100129292, RPS10, PTMA,RPS15A, HIST1H2BF, FAM131C, HIST1H2AM, SOX1, NME2P1, CTDSP1, COX8A,HLA-DPB1, HSPA8, EEF1A1, RPSA, NKX2-8, RPL13AP3, PPIA, KLF16, SERF2,RPS6, LRRC2

Example 38 Microarray Profiling of mRNA from Circulating Microvesicles(cMVs)

Large scale screening on high density arrays or mRNA levels within cMVscan be hindered by sample quantity and quality. A protocol was developedto allow robust analysis of cMV payload mRNAs that distinguish prostatecancer from normals.

cMVs were isolated from 1 ml of plasma from four prostate cancer andfour non-cancer control samples using filtration and concentration asdescribed in Example 6. RNA was extracted from 100 μl of plasmaconcentrate, which was then subdivided into 25 μl aliquots for lysiswith Trizol LS (Invitrogen, by life technologies, Carlsbad, Calif.)after treatment with RNASE A. The aqueous phase from each of the fouraliquots was precipitated with 70% ethanol, combined on a single Qiagenmini RNA extraction column (Qiagen, Inc., Valencia, Calif.), and elutedin a 30 μl volume. The eluted RNA can be difficult to reliably quantifyby standard means. Thus, a 10 μl volume was used for the subsequentlabeling reactions. Samples were cy-3 labeled with “Low Input Quick AmpLabeling” kit from Agilent for one-color gene expression analysisaccording to the manufacturer's instructions (Agilent Technologies,Santa Clara, Calif.), with the following modifications: 1) The spike-inmix for Cy3 labeling was altered so that the third dilution was 1:5 and1 μl was added to each sample; 2) 10 μl of sample was reduced in volumeto 2.5 μl using a vacufuge in duplicate for each sample; 3) Every samplewas processed in duplicate throughout the protocol until thepurification step of the amplified samples. At the beginning of thepurification protocol, the duplicate samples were combined andsubsequently passed through the column; 4) The samples were notquantified after purification but rather the full volume of the purifiedsample was hybridized to the array. Labeled samples were then hybridizedto Agilent Whole Genome 44K microarrays according to manufacturer'sinstructions (Agilent Technologies). Data was extracted with FeatureExtractor software (Agilent Technologies) and analyzed with GeneSpringGX (Agilent Technologies). Genes with expression in at least 50% of thesamples were included in the final analysis. 2155 probes were detectedthat met these criteria. Of these 2155, 24 were found to havesignificantly different expression (p value<0.05) between the prostatecancer group and the control group. See Table 25 and FIG. 22. Table 25shows 24 genes that were significantly differently expressed between themRNA payload from cMVs in the four prostate cancer patient samples andfour healthy control samples. FIG. 22 shows dot plots of raw backgroundsubtracted fluorescence values of selected genes from the microarray.

TABLE 25 Differentially expressed mRNAs in cMVs from PCa and healthysamples GeneSymbol p-value Change in normal FCAbsolute A2ML1 0.001 down1.88 GABARAPL2 0.002 up 1.36 PTMA 0.002 up 1.76 ETFB 0.003 up 1.16 RPL220.008 down 1.36 GUK1 0.009 up 1.28 PRDX5 0.011 up 1.48 HIST1H3B 0.014 up1.29 RABAC1 0.022 up 1.33 PTMA 0.024 up 1.65 C1orf162 0.026 down 1.35HLA-A 0.031 up 1.23 SEPW1 0.033 up 1.31 SOX1 0.034 down 1.38 EIF3C 0.034down 1.30 GZMH 0.037 up 1.81 CSDA 0.040 up 1.79 SAP18 0.040 down 1.36BAX 0.043 up 1.20 RABGAP1L 0.045 up 2.19 C10orf47 0.047 down 1.58HSP90AA1 0.047 up 1.46 PTMA 0.048 up 1.52 NRGN 0.049 up 2.57

Abbreviations in Table 25: “GeneSymbol” references nomenclatureavailable for each gene feature on the array. Details for each gene areavailable from Agilent (www.chem.agilent.com) or the HUGO database(www.genenames.org). “FCAbsolute” shows absolute fold-change in mRNAlevels detected between groups.

Example 39 Circulating Microvesicle Assay for Ovarian Cancer

In this Example, the vesicle ovarian cancer test is a microsphere basedimmunoassay for the detection of a set of protein biomarkers present onthe vesicles from plasma of patients with ovarian cancer. The testemploys antibodies or other ligand or binding agent (e.g., aptamer,peptides, peptid-nucleic acid) with binding specificity to the followingprotein biomarkers: CD95, CD9, CD59, CD63, CD81, and EpCAM. Aftercapture of the vesicles by antibody (or other binding agent) coatedmicrospheres to CD95 and EpCAM, phycoerythrin-labeled antibodies areused for the detection of general vesicle biomarkers (here CD9, CD59,CD63, and/or CD81). Depending on the level of binding of theseantibodies to the vesicles from a patient's plasma a determination ofthe presence or absence of ovarian cancer is made.

Vesicles are isolated as described above, e.g., in Examples 22 and 23.The profiling for such protein biomarkers can itself represent adiagnostic, prognostic or theranostic readout, by comparing the profilein a test sample to that of a reference sample. The reference sample canbe a level of microvesicles in a normal sample without cancer, whereinan elevated level of vesicles comprising CD95, CD9, CD59, CD63, CD81,and EpCAM indicates the presence of ovarian cancer.

In addition, the biomarkers are used to profile, identify or isolate aparticular test sample that can be further interrogated for additionalbiomarkers that may be present in or associated with the microvesiclepopulation. For example, the input sample of microvesicles is subjectedto an affinity or immunoprecipitation step using a binding agentspecific to a biomarker (here, substrate-bound antibody binding CD95and/or EpCam), and the isolated biomarker-positive (BM+) subpopulationis further processed using methods disclosed herein or known in the artto characterize and determine the presence of additional biomarkers(e.g., proteins, peptides, RNA, DNA) present in the subpopulation ofmicrovesicles.

The test can further comprises assessing levels of microRNA within thecaptured vesicles, using methodology presented herein, e.g., in Examples14-16. The microRNA comprises members of the miR200 family, includingmiR-200c. Decreased levels of the miR200 microRNA as compared to anon-cancer reference indicate the presence of ovarian cancer. Lowerlevels of miR200 further indicate a more aggressive cancer.

Example 40 miRs Differentially Expressed in PCa

Attempts to find a blood-based biomarker for prostate cancer (PCa)detection have been challenging. Quantification of microRNAs (miRs) inblood was used to identify potential genetic biomarkers. Usingplasma-derived circulating microvesicles (cMV) as an enriched source ofmiRs from cells, this Example illustrates a miR biosignature that candistinguish PCa samples from healthy controls as well as a miRbiosignature for metastatic PCa.

A panel of plasma samples from men with prostate cancers and controls(men biopsy confirmed without prostate cancer) were analyzed usingExiqon RT-PCR panels as described herein. Using the TNM scale, theprostate cancers included MX samples (did not evaluate distantmetastasis), M0 samples (no distant metastasis), and M1 samples(confirmed distant metastasis).

miRs were detected in vesicles isolated from the patient samples. RNAwas isolated from 150 μl of frozen plasma concentrate from each sampleusing a modified Qiagen miRneasy protocol (Qiagen GmbH, Germany). Themodified protocol included treating the concentrated samples with RnaseA before isolation so that only RNA protected within vesicles wasanalyzed in each sample. The samples were spiked with a known quantityof C. elegans microRNA for normalization in subsequent steps. 40 ng ofRNA isolated from vesicles in the sample was used for each Exiqon panel.

The Exiqon RT-PCR panel consisted of two 384 cards covering 750 miRs andcontrol assays. The qRT-PCR assay was performed using a Sybr green assayrun on an ABI 7900 (Life Technologies Corporation, Carlsbad, Calif.). Ctvalues for each miR assay were normalized to the Ct values ofinter-plate calibrator (IPC) probes and RT-PCR controls. Several qualitychecks were put into place. Samples were eliminated from analysis whenIPC Ct values were >25, RT-PCR Ct values were >35 and when samples didnot amplify control miRs (i.e., miR-16 and miR-21). Principal componentanalysis of the sample data was performed using GeneSpring software(Agilent Technologies, Inc., Santa Clara, Calif.) to identify outliers.Three samples were eliminated from the analysis due for failing toqualify using these quality measures.

Data was subjected to a paired t-test between sample groups as specifiedbelow and p-values were corrected with a Benjamini and Hochbergfalse-discovery rate test. miRs showing the most significant p-valueswere validated using a Taqman probe approach.

Ten of 750 miRs compared in non-metastatic PCa (n=64) and normal control(n=28) samples were found to have a >2.0-fold change with a Pvalue<0.01. See Table 26. In a validation set (N=168), expression ofhsa-miR-107 (P=0.03) and hsa-miR-574-3p (P=0.02) were examined. Bothwere significantly different between the non-metastatic PCa (n=133) andcontrol (n=35) samples.

TABLE 26 Non-metastatic prostate cancer vs control miR p-value FoldChange in Prostate Cancer hsa-miR-574-3p 0.003 3.32 hsa-miR-141 0.0083.22 hsa-miR-432 0.002 4.15 hsa-miR-326 0.001 6.36 hsa-miR-2110 0.0055.98 hsa-miR-181a-2* 0.004 −2.75 hsa-miR-107 0.000 13.16 hsa-miR-301a0.006 5.41 hsa-miR-484 0.009 2.92 hsa-miR-625* 0.003 4.00

Comparison of metastatic (n=15) and non-metastatic (n=55) samples foundthat 16 out of 750 miRs had a >2.0-fold change with a P value<0.01. SeeTable 27. Quantitation of these miRs in a subsequent validation set (39metastatic and 73 nonmetastatic) found that several miRs tested byqRT-PCR were able to distinguish metastatic and non-metastatic PCa(hsa-miR-200b, hsa-miR-375, hsa-miR-141, hsa-mir-331-3p, hsa-miR-181a,and hsa-miR-574-3p). In a separate cohort, hsa-miR-141 and hsa-miR-375levels were significantly higher in cMV from the serum of metastatic PCapatients (n=47) than in cMV of non-recurrent PCa patients (n=72;P=0.0001). See FIG. 23.

TABLE 27 Metastatic vs Non-Metastatic Prostate Cancer miR p-value FoldChange in Metastatic hsa-miR-582-3p 0.001 2.51 hsa-miR-20a* 0.002 3.62hsa-miR-375 0.003 10.71 hsa-miR-200b 0.003 3.90 hsa-miR-379 0.005 2.10hsa-miR-572 0.005 −7.39 hsa-miR-513a-5p 0.005 2.23 hsa-miR-577 0.0055.90 hsa-miR-23a* 0.005 2.30 hsa-miR-1236 0.005 2.63 hsa-miR-609 0.0062.31 hsa-miR-17* 0.006 4.80 hsa-miR-130b 0.007 6.12 hsa-miR-619 0.0083.37 hsa-miR-624* 0.009 6.09 hsa-miR-198 0.009 2.12

Blood-derived cMVs are a source of miR biomarkers for characterizing aphenotype. miRs biosignatures were able to distinguish non-metastaticPCa blood samples from controls. In metastatic plasma-derived cMVsamples, there was higher expression of 7 miRs, and 2 of these(hsa-miR-141 and hsa-miR-375) were further verified to be elevated inmetastatic serum-derived cMV. This Example provides blood-based miRbiosignatures of cMV for the detection of prostate cancer andidentification of metastatic cases.

Example 41 Isolating Subpopulations of Exosomes and Subsequent miRProfiles

In this Example, microRNA (miR) expression patterns were examined incirculating microvesicle subpopulations that were defined based onsurface protein composition. Vesicles isolated from a prostate cancercell line (VCaP) were flow sorted based on their surface proteincomposition using methodology as described herein. The vesicles wereevaluated for differential expression of miRs. Phycoerythrin-labeledantibodies targeting EpCam, CD63, or B7-H3 were used to sort thesubpopulations of vesicles by fluorescence-activated cell sorting.Vesicles were sorted on a Beckman-Coulter MoFlo XDP (Beckman Coulter,Inc., Brea, Calif.) so that each vesicle could be analyzed as anindividual particle. There was a significant shift in the intensity ofthe FL2 channel over the isotype control due to the abundance of theantigen on the surface of the vesicles. The sorted subpopulations ofvesicles were subsequently profiled by miR expression. The miR profilesfor the EpCam, CD63, and B7-H3 positive subpopulations were compared tothe profile of the total VCaP vesicle population. Differential miRexpression patterns were observed across the subpopulations and allexpression patterns were distinct from that observed in the totalpopulation. Patterns of both over- and under-expression of miRs wereobserved between groups. These data show that subpopulations of vesiclescan be distinguished and separated based on surface protein markers aswell as their genetic content, in this case miRs. The ability to isolatetissue-specific vesicle populations from patient plasma based on surfaceprotein composition and then analyze them based on both surface proteincomposition and genetic content can be used for diagnostic, prognostic,and theranostic applications as described herein.

Example 42 MicroRNA miR-497 for Detecting Lung Cancer

There is currently no blood test for the early diagnosis of lung cancer.MicroRNA was examined in circulating microvesicles (cMVs) isolated fromplasma samples. Vesicles were isolated as described in Example 6. RNAwas extracted from the vesicles contained in 1 ml of plasma using aTrizol method. MicroRNA payload was detected using quantitative Taqman®RT-PCR methodology. The expression of miR-497 was examined in plasmafrom 16 lung cancer patients and 15 control normal adults (i.e., no lungcancer). A significant difference in the copy number of miR-497 wasobserved between the two groups (p=0.0001). See FIG. 24A. Using athreshold of 1154 copies of miR-497 (in 0.1 ml of plasma) todifferentiate lung cancer versus normal samples (indicated by thevertical line in FIG. 24A), lung cancer was detected with 88%sensitivity and 80% specificity.

In a follow on study, circulating microvesicles (cMVs) from 24 non-smallcell lung cancer (NSCLC) patients of primarily early stage disease(Stage IA=9, IB=9, IIA=1, IIB=2, III=1, IV=2) and 26 healthy individualswere isolated from 1 ml of frozen plasma. The expression of miR-497 wasexamined in the cMVs from plasma samples from the lung cancer patientsand 26 control normal adults (i.e., no lung cancer). Patientcharacteristics are shown in Table 28.

TABLE 28 Patient Characteristics Stage Males Females Stage IA 5 4 StageIB 4 5 Stage IIA 1 0 Stage IIB 1 1 Stage III 1 0 Stage IV 0 2 Normal 1412

Median normalized copy number was 9000±307 copies per ml (±95% CIM) fornormal individuals and 27,500±1298 copies per ml (±95% CIM) for patientswith NSCLC. Setting a threshold for cancer of 1570 copies in 0.1 mlsamples (i.e., 15,700 copies per ml), the assay had a sensitivity of 79%and specificity of 81% and an AUC of 0.89. See results in FIGS. 24B-24Cand Table 29. Table 29 shows test performance using cut off thresholdsof 13,560 and 15,700 copies/ml. The threshold can be adjusted to favorsensitivity or specificity.

TABLE 29 miR-497 to Detect of Lung Cancer True Positive 21 19 TrueNegative 18 21 False Positive 8 5 False Negative 3 5 Sensitivity 88% 79%Specificity 69% 81% Accuracy 78% 80% AUC 0.89 0.89 Cut off 13,560 15,700(copies/ml)

Example 43 Prospective Analysis of a Circulating Biomarker DiagnosticAssay

Introduction:

With the exception of non-melanoma skin cancer, prostate cancer is themost common cancer affecting American men. In the United Stated in 2010,there were 217,730 new cases of prostate cancer and 32,050 deaths(source is the National Cancer Institute). The clinical behavior ofprostate cancer ranges from a microscopic well-differentiated tumor toan aggressive cancer with a high likelihood of invasion and metastasis.

Despite the significant contribution that the Prostate Specific Antigen(PSA) test has made to the effective management of prostate cancer, ithas been widely recognized as having significant shortcomings whichresult from the antigen being specific for prostate tissue and not forprostate cancer. A normal PSA value is currently considered to be lessthan 4.0 ng/mL, however, this cutoff remains controversial. If the serumPSA is in the range of 4.0 to 10 ng/mL there is an approximate 30%chance of finding prostate cancer on prostate biopsy even through theuse of repeated biopsies (e.g., 10-12 cores). A PSA cutoff of 2.5 ng/mLfor prostate biopsy has been recommended in the National ComprehensiveCancer Network (NCCN) guidelines. The American Cancer Society guidelinesrecommend considering a biopsy if the PSA is higher than 2.5 ng/mL.

Because the test is highly specific for the PSA antigen, it is elevatedin both prostate cancer and in non-malignant conditions such as benignprostatic hyperplasia (BPH) and prostatitis. Furthermore, not allprostate cancers release excessive levels of PSA into the serum and PSAlevels can be influenced by a variety of other factors such asconcomitant medications, age, and race (e.g., African Americans oftenhave relatively higher PSA levels; Asian men often have relatively lowerPSA levels). An elevated PSA, therefore, is associated with suboptimalclinical sensitivity, specificity, and positive predictive value as arisk assessment aid in the setting of possible prostate cancer. There isa need for a test to aid in the diagnosis of prostate cancer that addsspecificity to the current diagnostic algorithm.

Biology of Microvesicles:

Microvesicles can be created intracellularly by a variety of cell typeswhen a segment of the cell membrane spontaneously invaginates, undergoesexocytosis, and is released into the extracellular environment. Avariety of cell types may produce microvesicles including dendriticcells, tumor cells, lymphoid cells, mesothelial cells, epithelial cells,and cells from different tissues or organs. A microvesicle may includeany membrane-bound particle that is derived from either the plasmamembrane or an internal membrane and is subsequently released into theextracellular environment. Microvesicles are cell-derived structuresbounded by a lipid bilayer membrane arising from herniated evagination(blebbing), separation and sealing of portions of the plasma membrane,or from the export of any intracellular membrane-bounded vesicularstructure containing various membrane-associated proteins of cellularorigin. These may include surface-bound molecules derived from the hostcirculation that bind selectively to a tumor-derived protein as well asmolecules contained in the microvesicle or exosome lumen such astumor-derived miRNAs, mRNAs, and intracellular proteins. Microvesiclescan also include membrane fragments. Valadi et al. (2007) profiled thecomposition and contents of microvesicles derived from mast cells andfound them to be substantially enriched in microRNAs (miRNAs, miRs) andmessenger RNAs (mRNAs). In addition, the profile of RNAs found inmicrovesicles was different from the profile of RNAs found in thecytosol. For example, microvesicles contained no ribosomal RNAs, butthey contained large numbers of 19-22 nucleotide miRNAs. FIGS. 25A-Cshow a transmission electron micrograph of microvesicles isolated byultracentrifugation from a prostate cancer cell line grown in culture.FIG. 25A is an electron micrograph of Vcap-derived microvesicles boundto a glass slide, FIG. 25B is a scanning electron micrograph ofVcap-derived microvesicles, and FIG. 25C is a scanning electronmicrograph of Vcap microvesicles bound to a polystyrene bead coated withpoly-L-lysine.

The secretion of microvesicles by tumor cells and their implication inthe transport of proteins and nucleic acids (e.g. miRNAs) demonstrate arole for microvesicles in the pathological processes. Microvesicles havebeen found in a number of body fluids including, but not limited to,blood plasma, bronchoalveolar lavage fluid, and urine. Among otherbiological functions, microvesicles take part in intercellularcommunication as well as serving as transport vehicles for proteins,RNAs, DNAs, viruses, and prions.

Microvesicles and Biomarkers:

Protein biomarkers or tumor markers comprise protein molecules occurringin blood or tissue that are associated with cancer and whose measurementor identification is useful in disease diagnosis or clinical management.

Tumor markers can be used for a number of clinical purposes, includingwithout limitation the following: (1) Screening a healthy population ora high risk population for the presence of cancer, (2) As an aid inmaking a diagnosis of cancer or of a specific type of cancer, (3) As anaid in determining prognosis, and 4) To support treatment monitoring.

Research on biomarkers that support clinical decisions is increasingrapidly, and in the last few years, a variety of genetic biomarkers havebeen discovered and validated for use in guiding therapeutic decisionsfor oncology patients (e.g., KRAS in patients with colorectal cancer,Her2-neu over-expression in patients with breast cancer, and EGFR inpatients with non-small cell lung cancer). Many protein biomarkersavailable today, however, fail to demonstrate the sensitivity,specificity, and predictive value needed by clinicians to supportdecision-making. The carcinoembryonic antigen (CEA), for example, is aprotein that was first identified in patients with colorectal cancer,but has since been found to be elevated in a variety of malignanciesincluding pancreatic, gastric, lung, and breast as well as a variety ofbenign conditions such as hepatic cirrhosis, inflammatory bowel disease,chronic lung disease, and pancreatitis. Another example is CA-125, anantigen present on 80% of non-mucinous ovarian carcinomas, but it alsomay be elevated in other malignancies such as endometrial, pancreatic,lung, breast, and colon as well as a variety of benign conditions suchas menstruation, pregnancy, and endometriosis.

Microvesicles produced by tumor cells contain molecules of tumor-cellorigin such as miRNAs, mRNAs, and proteins. The isolation andconcentration of circulating microvesicles (cMV) can, therefore, presenta highly concentrated source of tumor-associated biomarkers.

This Example illustrates a protocol for developing a microvesicle-baseddiagnostic test that is characterized by a biomarker signature(biosignature) to provide improved assessment of presence and/or therisk of prostate cancer in men between the age of 40 and 75. Thismicrovesicle-based approach may further be used for staging/monitoringof neoplastic disease, supporting therapeutic decision-making, anddetermining prognosis.

As described herein, the invention provides in part a multiplex sandwichimmunoassay (described below) based on captured circulatingmicrovesicles that is capable of distinguishing plasma from men withorgan confined prostate cancer from men without prostate cancer. Thisassay comprises a microsphere-based immunoassay for the detection of aset of protein biomarkers present on the microvesicles in plasma frompatients with prostate cancer. A number of microvesicle surface antigenswere examined during assay development and an optimized biosignaturepanel or markers was selected. This preliminary approach employedspecific antibodies to the following protein biomarkers: CD9, CD63,CD81, PCSA, B7H3 and PSMA.

Both PSMA and PCSA are prostate specific markers used to isolatemicrovesicles secreted from prostate epithelial cells. B7-H3 is aprotein biomarker found in transformed cells and is used to identifymicrovesicles from cancer cells. CD9, CD63 and CD81 are tetraspanins ortransmembrane proteins found on most epithelial cells and onmicrovesicles secreted from epithelial cells. These tetraspanins act asgeneral vesicle markers (see Table 3). Phycoerythrin (PE) labeledanti-tetraspanin antibodies are used for the detection of the variousbound microvesicles in the assay. Depending on the level of binding ofthese antibodies to the microvesicles from a patient's plasma, adetermination of a correlation with the presence or risk of prostatecancer is made.

In a retrospective study comparing prostate cancer patients with men whodid not have prostate cancer this assay format showed an 83% sensitivityand 86% specificity. This biosignature will be tested with a set ofprospectively gathered samples from all men scheduled for a prostatebiopsy due to an elevated risk for prostate cancer.

In addition to the use of protein biomarkers, miRNA molecules will beadded to the assay to improve the sensitivity and specificity ofdetecting and differentiating prostate cancer. This will be accomplishedby collecting and concentrating the cMVs from plasma and extracting andmeasuring specific miRNA species and determining their correlation withprostate cancer. For example, miRNAs that have a high correlation withthe presence of prostate cancer or metastatic prostate cancer arepresented in the Examples above.

Objective:

The objective of this prospective study is to identify and/or confirm amicrovesicle-based prostate cancer specific biosignature that provides ahigh degree of accuracy in the detection of prostate cancer from a bloodsample. More specifically the objective is to develop an assay for whichwill be an aid in the detection of prostate cancer in a population ofmen referred to a urologist for assessment of possible prostate cancer.Assay performance targets include ≧80% sensitivity and ≧80% specificitywith an AUC of ≧0.80 on an ROC analysis based on the imperfect goldstandard of a ≧10 core ultrasound-guided biopsy.

Intended Use:

The circulating microvesicle (cMV) assay described in this Example isintended for the measurement of specified biomarkers in microvesicles inhuman plasma. The assay is intended to be used as an aid in thedetection of prostate cancer in men aged 40-79 years considered to be atelevated risk for prostate cancer with an elevated PSA and/or abnormaldigital rectal examination (DRE) and may be candidates for prostatebiopsy.

Study Design:

Blood samples will be collected from all men scheduled for a prostatebiopsy who meet the stated inclusion criteria. Samples will beaccessioned and stored in an appropriate format. Associated datacollected on the Case Report Forms will be stored electronically, andpaper copies will be filed accordingly. Blood will be processed intoplasma as specified in the sample collection protocol (see FIG. 25D),frozen and shipped from collection locations (e.g., hospital orcaregiver office) to the assay location where it will be processed andexamined for both protein and nucleic acid biomarkers. Circulatingmicrovesicles will be isolated and concentrated from plasma by adifferential filtration procedure. Concentrated microvesicles will beexamined for protein and miRNA biomarkers on a training set of at least50 prostate cancer samples from men with biopsy confirmed prostatecancer as well as at least 50 samples from men with a negative biopsyfrom the same location. Samples from at least 3 different collectionlocations across the United States will be used.

Both protein and RNAs will be examined for potential biomarkerscorrelated with the presence of PCa.

Methods:

Protein biomarker selection will be performed on a Luminex 200instrument system. Selected antibodies are conjugated to differentiallyaddressable microspheres from Luminex Corp. according to themanufacturer's recommended protocol. After conjugation, the coatedmicrospheres are washed, blocked by incubation in Starting BlockBlocking Buffer in PBS (Thermo Scientific, cat #37538), washed inphosphate buffered saline (PBS) and incubated with the concentrated cMVsfrom plasma as described below. Following capture of cMVs using beadbound anti-CD9, anti-B7H3, anti-PCSA and anti-PSMA, the microsphere-cMVcomplexes are washed and then incubated with phycoerythrin labeleddetector antibodies (PE-CD9, PE-CD63 and PE-CD81) and washed prior tobeing read on the Luminex 200. The standard protocol comprises measuringthe fluorescent signal from 100 microspheres and calculating the medianfluorescent intensity (MFI) for each differentially addressablemicrosphere, each corresponding to a different capture antibody. Variouscombinations of detector and capture antibodies will be examined inaddition to the tetraspanin detectors described above. For example,prostate or other marker biomarkers in Table 5 will be assessed asdesired.

Flow cytometry will be used to assay the total number of cMV in thevarious populations that are being assessed. Appropriate amounts ofplasma samples will be diluted 100 times in PBS and then incubated for15 min at room temperature in BD Trucount tubes (BD Biosciences, SanJose, Calif.) for quantification of events per sample. Trucount tubescontain an exactly number of fluorescent beads that can be compared withevents for each sample by flow cytometry. Sample acquisition by FACSCanto II cytometer (BD Biosciences) and later analysis by FlowJosoftware (Tree Star, Inc., Ashland, Oreg.) will reveal the number ofsample events and number of Trucount beads per tube. Finally,calculation of absolute number per sample will be obtained followinginstructions from BD and then adjusted by dilution factor.

MicroRNAs will also be examined from the cMVs from plasma samples. cMVsare concentrated and the miRNAs are extracted from the cMVs using aTrizol method. Briefly, cMVs are Rnase A (Epicentre Biotechnolgies,Madison, Wis.) treated (20 μg/ml for 20 min @ 37° C.) followed by Trizoltreatment (750 μl of Trizol LS to each 100 μl) and vortexed for 30 min.at 1400 rpm at room temperature. After centrifugation, the supernatantis collected and RNA is further purified with the miRNeasy 96 (QiagenInc., Valencia, Calif.) purification kit and stored at −80° C. 40 ng ofRNA are reverse transcribed and run on the Exiqon qRT-PCR Human panel Iand II (Exiqon, Inc, Woburn, Mass.) on an ABI 7900 (Applied Biosystems,Life Technologies, Carlsbad, Calif.). CT values are calculated by SDS2.4 software (Applied Biosystems). All samples are normalized to interplate calibrator and RT-PCR control.

Messenger RNA will also be examined from the cMVs from plasma samples.Messenger RNAs will be examined from the cMVs of plasma samples. First,cMVs will be isolated and treated with RNase A at 229 μg/ml for 20minutes at 37 C. Then the messenger RNA will be extracted using theTrizol method and purified with a Qiagen RNeasy mini kit precipitatingwith 70% ethanol. Sample RNA will be reverse transcribed and cy-3labeled using Agilent's “Low Input Quick Amp Labeling” kit for one-colorgene expression analysis according to the manufacturer's instructions.Labeled samples will be hybridized to Agilent's Whole Genome 44K v2arrays and washed according to manufacturer's specifications (AgilentTechnologies, Inc., Santa Clara, Calif.). Arrays will be scanned on anAgilent B scanner and data will be extracted with Feature Extractor(Agilent Technologies) software. Extracted data will be normalized witha global normalization method and analyzed with GeneSpring GX (AgilentTechnologies) software.

Both miRNA and messenger RNA will be examined from specificsubpopulations of cMVs from the plasma. For example, cMVs areconcentrated then the population that is positive for PCSA is isolatedusing magnetic immunoprecipitation. Following isolation the miRNAs areextracted using a modified Trizol method. Briefly, cMVs are Rnase A(Epicentre) treated (20 μg/ml for 20 min @ 37° C.) followed by Trizoltreatment (750 ul of Trizol LS to each 100 μl) and vortexed for 30 min.@ 1400 rpm at room temperature. After centrifugation, the supernatant iscollected and RNA is further purified with the miRNeasy 96 (Qiagen)purification kit and stored at −80° C. 40 ng of RNA are reversetranscribed and run on the Exiqon qRT-PCR Human panel I and II on an ABI7900. CT values are calculated by SDS 2.4 software (Applied Biosystems).All samples are normalized to inter plate calibrator and RT-PCR control,and/or the number of cMVs. Messenger RNAs will be examined from the cMVsof plasma samples. First, cMVs will be isolated and treated with RNase A(Epicentre) at 229 μg/ml for 20 minutes at 37 C. Then the messenger RNAwill be extracted using a modified Trizol method and purified with aQiagen RNeasy mini kit precipitating with 70% ethanol. Sample RNA willbe reverse transcribed and cy-3 labeled using Agilent's “Low Input QuickAmp Labeling” kit for one-color gene expression analysis according tothe manufacturer's instructions. Labeled samples will be hybridized toAgilent's Whole Genome 44K v2 arrays and washed according tomanufacturer's specifications. Arrays will be scanned on an Agilent Bscanner and data will be extracted with Feature Extractor (AgilentTechnologies) software. Extracted data will be normalized with a globalnormalization method and analyzed with GeneSpring GX (AgilentTechnologies) software.

Normalized analyte values will be imported into R (cran.org) and SASsoftware (SAS Institute Inc., Cary N.C.), subjected to quality controlanalysis and transformed prior to analysis. Analysis will proceed asfollows:

-   -   1) Signature performance evaluation (for pre-specified or novel        signatures)        -   a. This sample set may be used to evaluate the performance            of a signature that is fully specified prior to either the            unblinding of clinical outcome or laboratory testing of            samples. In such a case, the signature is considered            pre-specified and must be applied, unmodified, to new            analyte data on this sample set to obtain predicted outcomes            for all samples. Performance of the pre-specified signature            is evaluated by comparing predicted and true outcome (for            example, in terms of diagnostic sensitivity, specificity,            and accuracy). Statistics include performance estimates and            confidence intervals.        -   b. For signatures that are not pre-specified (i.e. that are            derived with foreknowledge of both clinical outcome and            laboratory testing results of samples), these samples may            still be used to evaluate the performance of the signature.            To ensure relatively unbiased estimates of performance,            statistical analyses will be performed nested within a            k-fold cross validation loop that will include all marker            selection and class prediction steps, as described below.    -   2) Marker selection for novel signatures        -   a. Markers are included in novel signatures only if they are            shown to be statistically informative by testing for their            association with disease outcome using a subset of commonly            applied techniques, e.g.            -   i. Welch test—robust parametric statistical test for                difference between group means when variances are                unequal.            -   ii. Wilcoxon signed-rank test—robust non-parametric                statistical test that can be interpreted as showing an                improvement in ROC AUC (above 0.50)            -   iii. Youden's J—calculated as the maximum combined                sensitivity and specificity for a marker, across all                possible diagnostic thresholds. Statistical significance                is evaluated via permutation tests.        -   b. Markers will only be judged statistically informative if            the test is significant in the context of the number            statistical tests performed. More specifically, we will            adjust comparison-wise p-values for multiple testing—e.g.            using false discovery rate thresholds or by control of            family-wise error rates.    -   3) Formation of novel signatures: Assuming a subset of        informative markers is identified in the preceding (marker        selection) stage, novel multi-marker models are formed using        well-established modeling techniques. Parameters for signatures        will be estimated by training the models on the full training        data set, and performance for the signature will be evaluated as        described under “Signature performance evaluation” using the        approach “for signatures that are not prespecified.” We will        focus on simple and well-established modeling techniques        including: discriminant analysis, support vector machines,        logistic regression, and decision trees. Results for all models        will be reported.

Additional a posteriori analyses may be performed on the data set forclinical variables of interest—for example, number of previous biopsies,indication for biopsy and biopsy result (e.g. high-grade prostaticintraepithelial neoplasia (HGPIN), atypical small acinar proliferation(ASAP), ATYPIA, benign prostatic hyperplasia (BPH) and prostatitis).Such analyses will be performed by introducing covariates orstratification variables into previously defined models. A posterioritests will be performed only after assessment of data sufficiency, alltests and results will be recorded, and P-values will be corrected formultiple testing.

Patient Eligibility:

Inclusion Criteria

-   -   1. Gender: Male    -   2. Age range 40 to 79 years    -   3. Any Race or Ethnicity    -   4. Men scheduled for a prostate biopsy as part of their routine        care and who agree to have their blood drawn within 7 days prior        to the scheduled biopsy.    -   5. Prostate biopsy pathology report available to submit to Caris        with all study forms and patient samples.    -   6. Level of comprehension to understand study and competence to        sign consent.

Exclusion Criteria

-   -   1. Any prior or ongoing treatment for prostate cancer including        prostatectomy or hormone therapy.    -   2. Previous diagnosis of cancer with the exception of prostate        cancer or non-melanoma skin cancer.    -   3. Prostate biopsy within 30 days of blood collection.    -   4. DRE performed on day of blood collection before the blood        draw was performed.    -   5. Decline phlebotomy.    -   6. Refusal to sign consent form.

The racial, gender (study limited to males) and ethnic characteristicsof the individuals eligible for participation in the Prostate BloodCollection Project shall reflect the demographics of subjects receivingor seeking urological medical care. Subjects are included in accordancewith these demographics. No individuals shall be excluded fromparticipation in the Prostate Blood Collection Project based on race,national origin, ethnicity, disability or HIV status.

Patient or Data Selection Requirements:

Data selection will be based on patient eligibility criteria and limitedto the subset of data records corresponding to subjects included in thisstudy (i.e. where laboratory analyte data is available). Data fieldsinclude those used for (non-PHI) donor identification, QC, and clinicalinterpretation as in Table 30:

TABLE 30 Patient Data Field description Comments PHI de-identifiedpatient Current biorepository donor barcode is sufficient identifierSite code (May be included in the above de-identified patient barcode)Race White, Black or African American, American Indian or Alaska Native,Native Hawaiian or Pacific Islander, Asian, Unknown Ethnicity Hispanicor Latino, Not Hispanic or Latino, Unknown Sex MUST BE MALE Age In years(not date of birth) Degree of inflammation Acute, Chronic, Mixed, NA(not applicable), UNK (unknown) DRE Result Normal; Abnormal, unilateral<50%; Abnormal, unilateral >50%; Abnormal, bilateral; NA Total PSA ng/mlFree PSA % Prostate Vol Cc PCA 3 Score Numeric; Unk; NA Reason forordering Abnormal % Free PSA, Abnormal DRE finding, Abnormal Imagingdata, Abnormal index biopsy PSA density, Abnormal PSA velocity, Activesurveillance, ASAP, Elevated PSA, Family history PCa, HGPIN, High PCA3,Rising PCA, Atypia Number of previous prostate biopsies Were anyprevious prostate biopsies positive Degree of inflammation Acute,Chronic, mixed, NA, Unk (associated with biopsy) Biopsy cores Positivebiopsy cores Primary Gleason Secondary Gleason Total Gleason AJCC StageTNM, Group Stage Pathological diagnosis Cancer, not cancer Month/Year ofdiagnosis (Not date of diagnosis, for HIPAA reasons) Number of samplessent Total samples sent, by tube type HGPIN result HGPIN or negative forHGPIN ASAP result ASAP or negative for ASAP Atypia result Atypia ornegative for Atypia Inflammation result Chronic, Acute, or Mixed Dataentered by Code indicating who entered data Data QC'd by Code indicatingwho performed QC on entered data Status Data partially entered,completely entered, QC'd, or similar

Patient or Data Collection Requirements:

The data fields will be captured on the clinical data form at thefacility where the blood is being drawn. Site personnel will use medicalrecords and patient derived information to capture all data elements.Data collected for each case will be entered into the database within 48hours of receipt. All data fields are required to be completed; if anyare not, a query is sent to the site and a response is requested in 10business days. Pre-selected data fields must be completed or the patientwill be excluded from analysis.

One of skill will appreciate that a similar protocol can be followed todevelop and confirm biosignatures comprising circulating biomarker inother settings, e.g., diagnostic, prognostic and/or theranosticassessment for other diseases and cancers than prostate cancer. Forexample, the biomarkers in Table 5 can be used as part of a biosignature for other settings.

Example 44 Data Mining to Identify Biomarkers

MicroRNAs are known to regulate the expression of mRNA. An expressiondatabase has been created that contains information about the mRNAexpression of many tumor types. The database contains data obtainedusing the Illumina DASL microarray (Illumina, Inc., San Diego, Calif.)for many thousands of patients. Circulating microvesicles (cMVs) containmicroRNA as the dominant RNA species and also contain mRNAs. In thisExample, an association was made between mRNA differentially expressedin cancer tumors from the expression database and those expressed incMVs. The mRNAs found differentially expressed in tumor tissue were alsoused to find microRNA targets in cMVs.

Gene expression data from the expression database was evaluated to findthe most statistically significant differentially expressed genesbetween prostate (PCa+), breast (BrCa), lung (LCa) and colorectalcancers (CRC) and matched normal tissue (PCa−), as well as between thecancer types (Table 31). Expression data (versions HT-12 and REF-8) forcancer samples (prostate, colorectal, breast, and lung) were analyzed todetect genes differentially expressed between cancer types. Similarly,prostate cancer (PCa) samples were compared against prostate normalsamples to detect prostate cancer specific probes. To perform theanalysis, expression data were normalized prior to analysis by adoptinga subset of 20 arbitrarily selected arrays (6 breast cancer, 5colorectal cancer, 5 lung cancer, and 4 prostate cancer) to generate aquantile reference distribution. All arrays in the data set were thennormalized against the reference distribution to ensure that each arrayshared the same quantile distribution. Next, normalized expression datawere analyzed for each probe in the data set. Differentially expressedprobes (and their corresponding genes) were detected by comparing eachpair of classes (e.g. prostate cancer vs. breast cancer, and prostatecancer vs. prostate normal) using a F-score (a.k.a. Fisher's score)statistic. This statistic, which measures between vs. within classvariation, was obtained by calculating the square of the mean groupdifference over the square of the sum of the group standard deviations.F-scores were set negative where the mean for the PCa+ samples was thelower of the two groups. Lastly, F-scores were sorted into descendingsequence using the absolute value of the F-score, and the top up/downregulated markers were chosen from the list.

TABLE 31 Most Statistically Significant Differentially Expressed GenesBetween PCa+ Samples and Indicated Samples Rank PCa− BrCa CRC LCa 1SEMG1 KLK2 KLK2 KLK2 2 MAP4K1 KLK2 KLK2 KLK2 3 CXCL13 MAOA KLK4 LRRC26 4GNAO1 KLK4 LRRC26 LOC389816 5 DST PVRL3 CDX1 KLK4 6 AQP2 SLC45A3 EEF1A2CAB39L 7 NELL2 NLGN4Y FOXA2 SPDEF 8 TNNT3 STX19 SPDEF SIM2 9 PRSS21CYorf14 BAIAP2L2 SLC45A3 10 SNAI2 C22orf32 FAM110B PNPLA7 11 BMP5 PNPLA7MIPOL1 TRIM36 12 PGF SIM2 CEACAM6 GSTP1 13 POU3F1 FEV SLC45A3 TRPV6 14ERCC1 TRPM8 ADRB2 ASTN2 15 TAF1C ARG2 LOC389816 MUC1 16 KLHL5 TRIM36C19orf33 MUC1 17 C16orf86 ADRB2 ZNF613 ZNF613 18 SMARCD3 LRRC26 TRIM36FAM110B 19 PENK EIF1AY ERN2 FEV 20 SCML1 SLC30A4 TRIM31 CRIP1 PCA+ LowerPCA+ Higher

For prostate cancer, a list of the most significantly over andunder-expressed genes was generated. These genes were compared to a listof mRNA that had been detected in cMVs from prostate cancer patients viamicroarray. One gene from the tissue list, AQP2, was also found to beexpressed in cMVs. The list of up- and down-regulated genes fromprostate tumor tissue was then mined using the TargetScan publicdatabase for microRNA that may influence the expression of these mRNAs.Matching microRNA was found for 11 of the 20 mRNA examined (Table 32).This list of microRNAs was then compared to a list of microRNAs that wefound to be reliably detected in cMVs. This comparison revealed that 10of the microRNAs that regulate the mRNA of interest in the prostatetumor tissue are also found in cMVs (Table 32).

TABLE 32 microRNA associated with differentially expressed mRNAsTargetScan Detected in TargetScan Detected in PCa Up result cMV? PCaDown result cMV? ADCYAP1R1 no target n/a SEMG1 no target n/a HECTD3miRs-26a + b yes MAP4K1 miR-342-5p no SLC44A4 no target n/a CXCL13miR-186 yes FASN miRs-15/16/ yes GNAO1 miR-1271 no 195/497/424 MPG notarget n/a DST miR-600 no MIR720 no target n/a AQP2 miR-216b no PTBP1miR-206 yes NELL2 miR-519 family no CPSF1 no target n/a TNNT3 no targetn/a C2orf56 no target n/a PRSS21 miR-206 yes HCRTR1 no target n/a SNAI2miR-203 yes

Additionally, mRNAs that are found to be differentially expressed areoften indicative of differences in the protein level. The results ofthis mining activity have identified proteins (e.g., KLK2) associatedwith cMVs that can be used to differentiate prostate cancer from othercancers, including breast, lung, and colon cancer. KLK2 is known to beassociated with prostatic tissue.

Example 45 microRNA Functional Assay

MicroRNAs can be found circulating in the blood encapsulated inmicrovesicles, HDL and LDL particles as well as components ofribonucleoprotein complexes (RNPs). microRNA can be detected usingavailable technologies such as RT-qPCR or next generation sequencing.However, microRNA that in a biologically active state are bound andactivated by one of the Argonaute proteins (Ago1-4). This Examplepresents an assay that can detect functional activity of a givenmicroRNA within a sample from various sources (including withoutlimitation cell lysates, bodily fluids, plasma, serum, isolatedmicrovesicles, etc) in a single reaction.

The assay comprises microbeads, a biotin conjugated synthetic RNAmolecule, streptavidin-PE, recombinant Argonaute 2 and RISC(RNA-InducedSilencing Complex) reaction buffer components. Components of the assayare shown in FIG. 26. As shown in FIG. 26A, the biotin conjugatedsynthetic RNA molecule contains a 3′ linker/extender region 262, acentral miRNA targeting region 263 and a second 5′ linker/extensionregion 264. The RNA is attached to a microbead 261 on the 3′ end and the5′ end is conjugated with biotin 266. The central miRNA targeting region263 is designed to complement a miRNA sequence of interest. Any microRNAof interest can be used in the assay; for the sake of example onlylet-7a is used here. Streptavidin-PE (Phycoerythrin) 265 is used tolabel the biotin end of the RNA. If target let-7a is present in thesample and is bound/associated with an Ago protein 267, e.g.,recombinant Agog (rAgo2), let-7a will bind the complementary microRNAtargeting region 263 and subsequently cleave the synthetic RNA at region263 through the endonucleolytic cleavage activity of Argonaute 2. Seestep 268 in FIG. 26. Once cleaved, the 5′ end of the synthetic RNAmolecule is released, thereby separating the biotin/Streptavidin-PEcomplex from the microbead 261. See FIG. 26B. Next, the microbeads areisolated and washed to remove the cleaved RNA, thereby leaving only theremaining uncleaved material as well as any cleaved RNA. After this washstep, the difference in PE signal correlates with the concentration andactivity of the Ago-bound target microRNA 267 present in the originalassay. In this Example, the quantity of Ago-bound let-7a in the inputsample determines the level of RNA cleaved. For example, if let-7a isnot present, the synthetic RNA target region 263 will remain uncleavedand the signal strength will be unchanged.

FIGS. 26C-E illustrate schematically various sources of RNA that can beused as input for the assay. FIG. 26C illustrates microRNA 268 bound toan Ago protein 269 to form a ribonucleic acid complex 267. FIG. 26Dillustrates immunoprecipitation of an Argonaute—microRNA complex 267using a binding agent to Ago 2610. FIG. 26E illustrates direct analysisof Argonaute—microRNA complex 267, e.g., from a cell lysate, bodilyfluid, or lysed microvesicle.

Although preferred embodiments of the present invention have been shownand described herein, it will be obvious to those skilled in the artthat such embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

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 17. A method of characterizing a cancer comprising, (a)isolating at least one nucleic acid-protein complex from a biologicalsample, wherein the at least one nucleic acid-protein complex comprisesat least one protein selected from the group consisting of an Argonautefamily member, Ago1, Ago2, Ago3, Ago4, GW182 (TNRC6A), TNRC6B, TNRC6C,HNRNPA2B1, HNRPAB, ILF2, NCL (Nucleolin), NPM1 (Nucleophosmin), RPL10A,RPL5, RPLP1, RPS12, RPS19, SNRPG, TROVE2, apolipoprotein, apolipoproteinA, apo A-I, apo A-II, apo A-IV, apo A-V, apolipoprotein B, apo B48, apoB100, apolipoprotein C, apo C-I, apo C-II, apo C-III, apo C-IV,apolipoprotein D (ApoD), apolipoprotein E (ApoE), apolipoprotein H(ApoH), apolipoprotein L, APOL1, APOL2, APOL3, APOL4, APOL5, APOL6,APOLD1, and a combination thereof; (b) determining a presence or levelof at least one nucleic acid biomarker within the at least one nucleicacid-protein complex; (c) identifying a biosignature comprising thepresence or level of the at least one nucleic acid biomarker; and (d)comparing the biosignature to a reference biosignature, wherein thecomparison is used to characterize a cancer.
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 19. Themethod of claim 17, wherein the nucleic acid-protein complex comprisesat least one protein selected from the group consisting of an Argonautefamily member, Ago1, Ago2, Ago3, Ago4, GW182 (TNRC6A), and a combinationthereof.
 20. The method of claim 17, wherein the nucleic acid-proteincomplex comprises at least one protein selected from the groupconsisting of Ago2, Apolipoprotein I, GW182 (TNRC6A), and a combinationthereof.
 21. The method of claim 17, wherein the at least one nucleicacid comprises at least one microRNA.
 22. The method of claim 21,wherein the at least one microRNA comprises a microRNA in Table
 5. 23.The method of claim 21, wherein the at least one microRNA comprises atleast one microRNA selected from the group consisting of miR-22, miR-16,miR-148a, miR-92a, miR-451, let7a, and a combination thereof.
 24. Themethod of claim 21, wherein the at least one nucleic acid-proteincomplex comprises at least one protein selected from the groupconsisting of Ago2, Apolipoprotein I, GW182 (TNRC6A), and a combinationthereof; and the at least one microRNA comprises at least one microRNAselected from the group consisting of miR-16, miR-92a, and a combinationthereof.
 25. (canceled)
 26. (canceled)
 27. (canceled)
 28. (canceled) 29.(canceled)
 30. (canceled)
 31. (canceled)
 32. (canceled)
 33. (canceled)34. (canceled)
 35. (canceled)
 36. (canceled)
 37. (canceled) 38.(canceled)
 39. (canceled)
 40. The method of claim 17, wherein thereference biosignature is from a subject without the cancer. 41.(canceled)
 42. The method of claim 17, wherein the comparing stepcomprises determining whether the biosignature is altered relative tothe reference biosignature, thereby providing a prognostic, diagnosticor theranostic determination for the cancer.
 43. The method of claim 17,wherein the biological sample comprises a bodily fluid.
 44. The methodof claim 43, wherein the bodily fluid comprises peripheral blood, sera,plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bonemarrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breastmilk, broncheoalveolar lavage fluid, semen, prostatic fluid, cowper'sfluid or pre-ejaculatory fluid, female ejaculate, sweat, fecal matter,hair, tears, cyst fluid, pleural and peritoneal fluid, pericardialfluid, lymph, chyme, chyle, bile, interstitial fluid, menses, pus,sebum, vomit, vaginal secretions, mucosal secretion, stool water,pancreatic juice, lavage fluids from sinus cavities, bronchopulmonaryaspirates, blastocyl cavity fluid, or umbilical cord blood.
 45. Themethod of claim 17, wherein the biological sample comprises urine, bloodor a blood derivative.
 46. (canceled)
 47. (canceled)
 48. (canceled) 49.The method of claim 17, wherein the at least one nucleic acid-proteincomplex is associated with a microvesicle population.
 50. (canceled) 51.(canceled)
 52. The method of claim 49, wherein the microvesiclepopulation is subjected to size exclusion chromatography, densitygradient centrifugation, differential centrifugation, nanomembraneultrafiltration, immunoabsorbent capture, affinity purification,affinity capture, immunoassay, microfluidic separation, flow cytometryor combinations thereof.
 53. The method of claim 49, wherein themicrovesicle population is contacted with at least one binding agent.54. The method of claim 53, wherein the at least one binding agentcomprises a nucleic acid, DNA molecule, RNA molecule, antibody, antibodyfragment, aptamer, peptoid, zDNA, peptide nucleic acid (PNA), lockednucleic acid (LNA), lectin, peptide, dendrimer, membrane proteinlabeling agent, chemical compound, or a combination thereof.
 55. Themethod of claim 53, wherein the at least one binding agent is used tocapture and/or detect the microvesicle population.
 56. (canceled) 57.(canceled)
 58. The method of claim 55, wherein the at least one bindingagents binds at least one of CD9, CD63, CD81, PSMA, PCSA, B7H3 andEpCam.
 59. The method of claim 55, wherein the at least one bindingagents binds at least one of a tetraspanin, CD9, CD63, CD81, CD63, CD9,CD81, CD82, CD37, CD53, Rab-5b, Annexin V, MFG-E8, or a protein in Table3.
 60. (canceled)
 61. (canceled)
 62. The method of claim 49, wherein theat least one nucleic acid-protein complex comprises payload within themicrovesicle population.
 63. (canceled)
 64. (canceled)
 65. (canceled)66. (canceled)
 67. The method of claim 17, wherein the cancer comprisesprostate cancer.
 68. (canceled)
 69. (canceled)
 70. (canceled) 71.(canceled)
 72. (canceled)
 73. (canceled)
 74. (canceled)
 75. (canceled)76. (canceled)
 77. (canceled)
 78. (canceled)
 79. (canceled) 80.(canceled)
 81. (canceled)
 82. (canceled)
 83. (canceled)
 84. (canceled)85. (canceled)
 86. (canceled)
 87. (canceled)
 88. (canceled) 89.(canceled)
 90. (canceled)
 91. (canceled)
 92. (canceled)
 93. (canceled)94. (canceled)
 95. (canceled)
 96. (canceled)
 97. (canceled) 98.(canceled)
 99. (canceled)
 100. (canceled)
 101. (canceled) 102.(canceled)
 103. (canceled)
 104. (canceled)